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R/methods_peakPantheRAnnotation.R
In peakPantheR: Peak Picking and Annotation of High Resolution Experiments
Defines functions
rtCorrection_diagnosticPlot
rtCorrection_prepareAnnotation
rtCorrection_prepareTargetFeatTable
rtCorrection_checkInput
resetAnnot_useUROIuseFIR
resetAnnot_uROIExist
resetAnnot_spectraPathMetadata
resetAnnot_newTargetFeatTable
resetAnnot_prevTargetFeatTable
resetAnnot_targetFeatTable_uROI_FIR_cpdMeta
outputAnnotationResult_saveSummary
outputAnnotationResult_savePeaktable
outputAnnotationResult_saveSpectraMetadata
outputAnnotationResult_saveCpdMetadata
outputAnnotationDiagnostic_saveSingleMultiPlot
singleDiagnosticPlots
annotationParamsDiagnostic_FIR
annotationParamsDiagnostic_uROI
subsetting_peakTables_dataPoints_peakFit
#####################################################################
## Constructor for \link{peakPantheRAnnotation-class}, see function
# peakPantheRAnnotation() for the initialisation checks
setMethod("initialize", "peakPantheRAnnotation",
function(.Object, ...) {
## load ... arguments
.Object <- methods::callNextMethod(.Object, ...)
# Check the validity of results
methods::validObject(.Object)
return(.Object)
})
#####################################################################
## show method for \link{peakPantheRAnnotation-class}
setMethod("show",
signature = "peakPantheRAnnotation",
definition = function(object) {
cat("An object of class ", class(object), "\n", sep = "")
cat(" ", length(object@cpdName), " compounds in ",
length(object@filepath), " samples. \n", sep = "")
if (object@uROIExist) {
cat(" updated ROI exist (uROI)\n", sep = "")
} else {
cat(" updated ROI do not exist (uROI)\n", sep = "")
}
if (object@useUROI) {
cat(" uses updated ROI (uROI)\n", sep = "")
} else {
cat(" does not use updated ROI (uROI)\n", sep = "")
}
if (object@useFIR) {
cat(" uses fallback integration regions (FIR)\n", sep = "")
} else {
cat(" does not use fallback integration regions (FIR)\n", sep = "")
}
if (object@isAnnotated) {
cat(" is annotated\n", sep = "")
} else {
cat(" is not annotated\n", sep = "")
}
invisible(NULL)
})
#####################################################################
## validObject method for \link{peakPantheRAnnotation-class}.
# Number of compounds based on @cpdID length, number of samples based on
# @filepath length. Slot type is not checked as \code{setClass} enforces it.
# peakTables, dataPoints and peakFit type are checked on first list element.
setValidity("peakPantheRAnnotation",
function(object) valid_peakPantheRAnnotation(object))
#####################################################################
## Accessors
#####################################################################
# cpdID
setGeneric("cpdID", function(object, ...) standardGeneric("cpdID"))
#' cpdID accessor
#' @param object peakPantheRAnnotation
#' @return (str) A character vector of compound IDs, of length number of
#' compounds
#' @docType methods
#' @aliases cpdID
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin',
#' 'mz', 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' cpdID(annotation)
#' # [1] 'ID-1' 'ID-2'
#' }
setMethod("cpdID", "peakPantheRAnnotation", function(object) {
object@cpdID
})
# cpdName
setGeneric("cpdName", function(object, ...) standardGeneric("cpdName"))
#' cpdName accessor
#' @param object peakPantheRAnnotation
#' @return (str) A character vector of compound names, of length number of
#' compounds
#' @docType methods
#' @aliases cpdName
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' cpdName(annotation)
#' # [1] 'Cpd 1' 'Cpd 2'
#' }
setMethod("cpdName", "peakPantheRAnnotation", function(object) {
object@cpdName
})
# ROI targetFeatTable with ROI
setGeneric("ROI", function(object, ...) standardGeneric("ROI"))
#' ROI accessor returns targetFeatTable with cpdID, cpdName added
#' @param object peakPantheRAnnotation
#' @return (data.frame) target feature table with compounds as row and ROI
#' parameters as columns
#' @docType methods
#' @aliases ROI
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ROI(annotation)
#' # rtMin rt rtMax mzMin mz mzMax cpdID cpdName
#' # 1 3310 3344.888 3390 522.1948 522.2 522.2052 ID-1 Cpd 1
#' # 2 3280 3385.577 3440 496.1950 496.2 496.2050 ID-2 Cpd 2
#' }
setMethod("ROI", "peakPantheRAnnotation", function(object) {
out <- object@ROI
out$cpdID <- object@cpdID
out$cpdName <- object@cpdName
return(out)
})
# uROI targetFeatTable with uROI
setGeneric("uROI", function(object, ...) standardGeneric("uROI"))
#' uROI accessor returns targetFeatTable with cpdID, cpdName added
#' @param object peakPantheRAnnotation
#' @return (data.frame) target feature table with compounds as row and uROI
#' parameters as columns
#' @docType methods
#' @aliases uROI
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' uROI(annotation)
#' # rtMin rt rtMax mzMin mz mzMax cpdID cpdName
#' # 1 NA NA NA NA NA NA ID-1 Cpd 1
#' # 2 NA NA NA NA NA NA ID-2 Cpd 2
#' }
setMethod("uROI", "peakPantheRAnnotation", function(object) {
out <- object@uROI
out$cpdID <- object@cpdID
out$cpdName <- object@cpdName
return(out)
})
# FIR similar to targetFeatTable with FIR
setGeneric("FIR", function(object, ...) standardGeneric("FIR"))
#' FIR accessor returns targetFeatTable with cpdID, cpdName added
#' @param object peakPantheRAnnotation
#' @return (data.frame) target feature table with compounds as row and FIR
#' parameters as columns
#' @docType methods
#' @aliases FIR
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' FIR(annotation)
#' # rtMin rtMax mzMin mzMax cpdID cpdName
#' # 1 NA NA NA NA ID-1 Cpd 1
#' # 2 NA NA NA NA ID-2 Cpd 2
#' }
setMethod("FIR", "peakPantheRAnnotation", function(object) {
out <- object@FIR
out$cpdID <- object@cpdID
out$cpdName <- object@cpdName
return(out)
})
# filepath
setGeneric("filepath", function(object, ...) standardGeneric("filepath"))
#' filepath accessor
#' @param object peakPantheRAnnotation
#' @return (str) A character vector of file paths, of length number of spectra
#' files
#' @docType methods
#' @aliases filepath
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#' filepath(annotation)
#' # [1] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko15.CDF'
#' # [2] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko16.CDF'
#' # [3] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko18.CDF'
#' }
setMethod("filepath", "peakPantheRAnnotation", function(object) {
object@filepath
})
# cpdMetadata
setGeneric("cpdMetadata",
function(object, ...) standardGeneric("cpdMetadata"))
#' cpdMetadata accessor
#' @param object peakPantheRAnnotation
#' @return (data.frame) A data.frame of compound metadata, with compounds as row
#' and metadata as columns
#' @docType methods
#' @aliases cpdMetadata
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values not initialised
#' cpdMetadata(annotation)
#' # data frame with 0 columns and 2 rows
#' }
setMethod("cpdMetadata", "peakPantheRAnnotation", function(object) {
object@cpdMetadata
})
# spectraMetadata
setGeneric("spectraMetadata",
function(object, ...) standardGeneric("spectraMetadata"))
#' spectraMetadata accessor
#' @param object peakPantheRAnnotation
#' @return (data.frame) A data.frame of sample metadata, with samples as row and
#' metadata as columns
#' @docType methods
#' @aliases spectraMetadata
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values not initialised
#' spectraMetadata(annotation)
#' # data frame with 0 columns and 3 rows
#' }
setMethod("spectraMetadata", "peakPantheRAnnotation",
function(object) {
object@spectraMetadata
})
# acquisitionTime return converted to POSIXct
setGeneric("acquisitionTime",
function(object, ...) standardGeneric("acquisitionTime"))
#' acquisitionTime accessor returns value as.POSIXct
#' @param object peakPantheRAnnotation
#' @return (POSIXct) A character vector of acquisition date-time (converted from
#' POSIXct) or NA
#' @docType methods
#' @aliases acquisitionTime
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## acquisitionTime can only be extracted from NetCDF files
#' acquisitionTime(annotation)
#' # [1] NA NA NA
#' }
setMethod("acquisitionTime", "peakPantheRAnnotation",
function(object) {
as.POSIXct(object@acquisitionTime)
})
# uROIExist
setGeneric("uROIExist", function(object, ...) standardGeneric("uROIExist"))
#' uROIExist accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if uROI have been set
#' @docType methods
#' @aliases uROIExist
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' uROIExist(annotation)
#' # [1] FALSE
#' }
setMethod("uROIExist", "peakPantheRAnnotation", function(object) {
object@uROIExist
})
# useUROI
setGeneric("useUROI", function(object, ...) standardGeneric("useUROI"))
#' useUROI accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if uROI are to be used
#' @docType methods
#' @aliases useUROI
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' useUROI(annotation)
#' # [1] FALSE
#' }
setMethod("useUROI", "peakPantheRAnnotation", function(object) {
object@useUROI
})
# useFIR
setGeneric("useFIR", function(object, ...) standardGeneric("useFIR"))
#' useFIR accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if FIR are to be used
#' @docType methods
#' @aliases useFIR
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' useFIR(annotation)
#' # [1] FALSE
#' }
setMethod("useFIR", "peakPantheRAnnotation", function(object) {
object@useFIR
})
# TIC
setGeneric("TIC", function(object, ...) standardGeneric("TIC"))
#' TIC accessor
#' @param object peakPantheRAnnotation
#' @return (float) A numeric vector of Total Ion Chromatogram or NA, of length
#' number of spectra files
#' @docType methods
#' @aliases TIC
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' TIC(annotation)
#' # [1] NA NA NA
#' }
setMethod("TIC", "peakPantheRAnnotation", function(object) {
object@TIC
})
# peakTables
setGeneric("peakTables", function(object, ...) standardGeneric("peakTables"))
#' peakTables accessor with cpdID and cpdName added back
#' @param object peakPantheRAnnotation
#' @return (data.frame) A list of peakTable data.frame, of length number of
#' spectra files. Each peakTable data.frame has compounds as rows and peak
#' annotation results as columns, with added compound ID and name.
#' @docType methods
#' @aliases peakTables
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' peakTables(annotation)
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' # [[3]]
#' # NULL
#' }
setMethod("peakTables", "peakPantheRAnnotation", function(object) {
tmpPeakTables <- lapply(object@peakTables, function(x) {
if (!is.null(x)) {
return(cbind.data.frame(x, cpdID = object@cpdID,
cpdName = object@cpdName,
stringsAsFactors = FALSE))
} else {
return(NULL)
}
})
return(tmpPeakTables)
})
# dataPoints
setGeneric("dataPoints", function(object, ...) standardGeneric("dataPoints"))
#' dataPoints accessor
#' @param object peakPantheRAnnotation
#' @return A list of length number of spectra files. Each list element is a
#' \emph{ROIsDataPoint} list of \code{data.frame} of raw data points for each
#' ROI/uROI (retention time 'rt', mass 'mz' and intensity 'int' (as column) of
#' each raw data points (as row))
#' @docType methods
#' @aliases dataPoints
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' dataPoints(annotation)
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' # [[3]]
#' # NULL
#' }
setMethod("dataPoints", "peakPantheRAnnotation", function(object) {
object@dataPoints
})
# peakFit
setGeneric("peakFit", function(object, ...) standardGeneric("peakFit"))
#' peakFit accessor
#' @param object peakPantheRAnnotation
#' @return A list of length number of spectra files. Each list element is a
#' \emph{curveFit} list of \code{peakPantheR_curveFit} or NA for each ROI
#' @docType methods
#' @aliases peakFit
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' peakFit(annotation)
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' # [[3]]
#' # NULL
#' }
setMethod("peakFit", "peakPantheRAnnotation", function(object) {
object@peakFit
})
# isAnnotated
setGeneric("isAnnotated", function(object, ...) standardGeneric("isAnnotated"))
#' isAnnotated accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if the annotation has taken place
#' @docType methods
#' @aliases isAnnotated
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' isAnnotated(annotation)
#' # [1] FALSE
#' }
setMethod("isAnnotated", "peakPantheRAnnotation", function(object) {
object@isAnnotated
})
# nbSamples
setGeneric("nbSamples", function(object, ...) standardGeneric("nbSamples"))
#' nbSamples accessor established on filepath
#' @param object peakPantheRAnnotation
#' @return (int) number of samples
#' @docType methods
#' @aliases nbSamples
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' nbSamples(annotation)
#' # [1] 3
#' }
setMethod("nbSamples", "peakPantheRAnnotation", function(object) {
return(length(object@filepath))
})
# nbCompounds
setGeneric("nbCompounds", function(object, ...) standardGeneric("nbCompounds"))
#' nbCompounds accessor established on cpdID
#' @param object peakPantheRAnnotation
#' @return (int) number of samples
#' @docType methods
#' @aliases nbCompounds
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' nbCompounds(annotation)
#' # [1] 2
#' }
setMethod("nbCompounds", "peakPantheRAnnotation", function(object) {
return(length(object@cpdID))
})
# annotationTable
setGeneric("annotationTable",
function(object, column) standardGeneric("annotationTable"))
#' @title annotationTable accessor
#' @description annotationTable returns a dataframe (row samples, col compounds)
#' filled with a specific peakTable column
#' @param object peakPantheRAnnotation
#' @param column a peakTable columns
#' @return (data.frame) (row samples, col compounds) filled with a specific
#' peakTable column
#' @docType methods
#' @aliases annotationTable
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' annotationTable(annotation)
#' # ID-1 ID-2
#' # C:/R/R-3.6.0/library/faahKO/cdf/KO/ko15.CDF NA NA
#' # C:/R/R-3.6.0/library/faahKO/cdf/KO/ko16.CDF NA NA
#' # C:/R/R-3.6.0/library/faahKO/cdf/KO/ko18.CDF NA NA
#' }
setMethod("annotationTable", "peakPantheRAnnotation",
function(object, column) {
## Expect the object to be valid, therefore peakTables is a list of NULL or
## data.frame
nbCpd <- length(object@cpdID)
nbSample <- length(object@filepath)
## Exit with empty data.frame if no samples or only NULL
if (nbSample < 1) {
# an empty data.frame
tmpAnnotation <- data.frame(matrix(vector(), nbSample, nbCpd),
stringsAsFactors = FALSE)
rownames(tmpAnnotation) <- object@filepath
colnames(tmpAnnotation) <- object@cpdID
return(tmpAnnotation)
}
if (is.null(object@peakTables[[1]])) {
# an empty data.frame
tmpAnnotation <- data.frame(matrix(vector(), nbSample, nbCpd),
stringsAsFactors = FALSE)
rownames(tmpAnnotation) <- object@filepath
colnames(tmpAnnotation) <- object@cpdID
return(tmpAnnotation)
}
## Check the column exist
if (!(column %in% colnames(object@peakTables[[1]]))) {
stop("input column is not a column of peakTables")
}
## Concatenate all the results in a single data.frame
tmpAnnotation <- vector("list", nbSample)
for (fl in seq_len(nbSample)) {
tmpAnnotation[fl] <- object@peakTables[[fl]][column]
}
tmpAnnotation <- data.frame(t(do.call("cbind", tmpAnnotation)))
rownames(tmpAnnotation) <- object@filepath
colnames(tmpAnnotation) <- object@cpdID
return(tmpAnnotation)
})
# EICs
setGeneric("EICs",
function(object, aggregationFunction = "sum", ...)
standardGeneric("EICs"))
#' EICs accessor
#' @param object peakPantheRAnnotation
#' @param aggregationFunction (str) Function to use in order to aggregate
#' intensities across mz in each scan. One of \code{sum}, \code{max},
#' \code{min}, \code{mean}
#' @return (float) Extracted Ion Chromatogram aggregated across mz in each scan
#' @docType methods
#' @aliases EICs
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' EICs(annotation)
#' # [[1]]
#' # list()
#' # [[2]]
#' # list()
#' # [[3]]
#' # list()
#' }
setMethod("EICs", "peakPantheRAnnotation",
function(object, aggregationFunction) {
tmpEICs <- lapply(object@dataPoints, function(ROIsDataPoint) {
lapply(ROIsDataPoint, function(x) {
generateIonChromatogram(x,aggregationFunction = aggregationFunction)
})
})
return(tmpEICs)
})
# filename
setGeneric("filename", function(object, ...) standardGeneric("filename"))
#' filename accessor by spliting filepath
#' @param object peakPantheRAnnotation
#' @return (str) filename
#' @docType methods
#' @aliases filename
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' filename(annotation)
#' # [1] 'ko15' 'ko16' 'ko18'
#' }
setMethod("filename", "peakPantheRAnnotation", function(object) {
return(tools::file_path_sans_ext(basename(object@filepath)))
})
#####################################################################
# Sub-setting object
#####################################################################
#' extract parts of peakPantheRAnnotation class
#' @param x object from which to extract element(s) or in which to replace
#' element(s).
#' @param i (sample) indices specifying elements to extract or replace
#' @param j (compound) indices specifying elements to extract or replace
#' @param drop not applicable
#' @return (peakPantheRAnnotation) object subset
#'
#' @aliases [,peakPantheRAnnotation-method
#' @docType methods
#'
setMethod("[", "peakPantheRAnnotation",
function(x, i, j, drop = "missing") {
## i is row, samples j is col, compounds
# check inputs and fallback
if (missing(i) & missing(j)) { return(x) }
if (missing(i)) { i <- seq_len(nbSamples(x)) }
if (missing(j)) { j <- seq_len(nbCompounds(x)) }
# check dim size
if (max(i) > nbSamples(x)) {
stop(paste("i index out of bound: maximum", nbSamples(x))) }
if (max(j) > nbCompounds(x)) {
stop(paste("j index out of bound: maximum", nbCompounds(x))) }
# sub-setting
.cpdID <- x@cpdID[j]
.cpdName <- x@cpdName[j]
.ROI <- x@ROI[j, , drop = FALSE]
.FIR <- x@FIR[j, , drop = FALSE]
.uROI <- x@uROI[j, , drop = FALSE]
.filepath <- x@filepath[i]
.cpdMetadata <- x@cpdMetadata[j, , drop = FALSE]
.spectraMetadata <- x@spectraMetadata[i, , drop = FALSE]
.acquisitionTime <- x@acquisitionTime[i]
.uROIExist <- x@uROIExist
.useUROI <- x@useUROI
.useFIR <- x@useFIR
.TIC <- x@TIC[i]
.isAnnotated <- x@isAnnotated
# peakTables, dataPoints & peakFit
subRes <- subsetting_peakTables_dataPoints_peakFit(x, i, j)
.peakTables <- subRes$tmp_peakTables
.dataPoints <- subRes$tmp_dataPoints
.peakFit <- subRes$tmp_peakFit
# load value in new object that will need to pass validObject()
peakPantheRAnnotation(cpdID = .cpdID, cpdName = .cpdName, ROI = .ROI,
FIR = .FIR, uROI = .uROI, filepath = .filepath,
cpdMetadata = .cpdMetadata, spectraMetadata = .spectraMetadata,
acquisitionTime = .acquisitionTime, uROIExist = .uROIExist,
useUROI = .useUROI, useFIR = .useFIR, TIC = .TIC,
peakTables = .peakTables, dataPoints = .dataPoints, peakFit = .peakFit,
isAnnotated = .isAnnotated)
})
# sub-setting peakTables, dataPoints and peakFit
subsetting_peakTables_dataPoints_peakFit <- function(x, i, j) {
# peakTables, filter samples first, then compounds in each table
tmp_peakTables <- x@peakTables[i]
if (all(vapply(tmp_peakTables, is.null, FUN.VALUE = logical(1)))) {
# no cpd filter if all NULL
.peakTables <- tmp_peakTables
} else {
# cpd filter in each table
.peakTables <- lapply(tmp_peakTables, function(x, y) {
x[y, ]
}, y = j)
}
# dataPoints, filter samples first, then compounds in each ROIsDataPoint
tmp_dataPoints <- x@dataPoints[i]
if (all(vapply(tmp_dataPoints, is.null, FUN.VALUE = logical(1)))) {
# no cpd filter if all NULL
.dataPoints <- tmp_dataPoints
} else {
# cpd filter in each ROIsDataPoint
.dataPoints <- lapply(tmp_dataPoints, function(x, y) {
x[y]
}, y = j)
}
# peakFit, filter samples first, then compounds in each curveFit list
tmp_peakFit <- x@peakFit[i]
if (all(vapply(tmp_peakFit, is.null, FUN.VALUE = logical(1)))) {
# no cpd filter if all NULL
.peakFit <- tmp_peakFit
} else {
# cpd filter in each curveFit list
.peakFit <- lapply(tmp_peakFit, function(x, y) {
x[y]
}, y = j)
}
return(list(tmp_peakTables = .peakTables, tmp_dataPoints = .dataPoints,
tmp_peakFit = .peakFit))
}
#####################################################################
## Fit diagnosis
#####################################################################
## Set uROI and FIR based on annotation results
setGeneric("annotationParamsDiagnostic",
function(object, verbose = TRUE, ...)
standardGeneric("annotationParamsDiagnostic"))
#' @title Set uROI and FIR based on annotation results
#' @description Set updated ROI (uROI) and Fallback Integration Regions (FIR)
#' based on the annotation results. If the object is not annotated, it is
#' returned untouched. ROI is not modified. If uROI exist they are left
#' untouched, otherwise they are set as the minimum and maximum found peaks
#' limits (+/-5\% of ROI in retention time). If FIR are used they are left
#' untouched, otherwise they are set as the median of the found limits (rtMin,
#' rtMax, mzMin, mzMax).
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param verbose (bool) If TRUE message progress of uROI and FIR calculation
#' @return (peakPantheRAnnotation) object with updated ROI and FIR set from
#' annotation results
#' @docType methods
#' @aliases annotationParamsDiagnostic
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' annotationParamsDiagnostic(emptyAnnotation, verbose=TRUE)
#' # Warning: the object has not been annotated, return the object untouched
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 3 samples.
#' # updated ROI do not exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
#' }
setMethod("annotationParamsDiagnostic", "peakPantheRAnnotation",
function(object, verbose) {
# init
outAnnotation <- object
# not annotated, pass
if (!outAnnotation@isAnnotated) {
if (verbose) {
message('Warning: the object has not been annotated, return',
' the object untouched') }
return(outAnnotation) }
# uROI uROI doesn't exist, set uROI with min/max of found peaks (if NA, use
# ROI value)
if (!outAnnotation@uROIExist) {
outAnnotation <- annotationParamsDiagnostic_uROI(outAnnotation, verbose)
} else { # uROI exist (even not used), no replacement
if (verbose) { message("uROI already exist, will not be changed") }
}
# FIR FIR not used, recalculate (if NA, use uROI value that was set
# previously)
if (!outAnnotation@useFIR) {
outAnnotation <- annotationParamsDiagnostic_FIR(outAnnotation, verbose)
} else { # FIR used, do not recalculate
if (verbose) { message("FIR in use, will not be changed") }
}
return(outAnnotation)
})
# annotationParamsDiagnostic for uROI
annotationParamsDiagnostic_uROI <- function(outAnnotation, verbose) {
if (verbose) { message('uROI will be set as mimimum/maximum of',
' found peaks (+/-5% of ROI in retention time)') }
# rt ROI 5% (no NA in ROI rtMin/rtMax)
rtMargin <- (ROI(outAnnotation)$rtMax - ROI(outAnnotation)$rtMin) * 0.05
# rtMin (min found peak -5% of ROI)
rtMinUROI <- unname(vapply(annotationTable(outAnnotation,"rtMin"), min,
na.rm = TRUE, FUN.VALUE = numeric(1)))
rtMinUROI <- rtMinUROI - rtMargin
if (sum(is.infinite(rtMinUROI)) != 0) {
if (verbose) { message('uROI min rtMin which are NA are',
' replaced with ROI rtMin') }
rtMinUROI[is.infinite(rtMinUROI)] <-
outAnnotation@ROI[is.infinite(rtMinUROI), "rtMin"] }
# rtMax (max found peak +5% of ROI)
rtMaxUROI <- unname(vapply(annotationTable(outAnnotation,"rtMax"), max,
na.rm = TRUE, FUN.VALUE = numeric(1)))
rtMaxUROI <- rtMaxUROI + rtMargin
if (sum(is.infinite(rtMaxUROI)) != 0) {
if (verbose) { message('uROI max rtMax which are NA are',
' replaced with ROI rtMax') }
rtMaxUROI[is.infinite(rtMaxUROI)] <-
outAnnotation@ROI[is.infinite(rtMaxUROI), "rtMax"] }
# mzMin
mzMinUROI <- unname(vapply(annotationTable(outAnnotation,"mzMin"), min,
na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.infinite(mzMinUROI)) != 0) {
if (verbose) {
message("uROI min mzMin which are NA are replaced ROI mzMin") }
mzMinUROI[is.infinite(mzMinUROI)] <-
outAnnotation@ROI[is.infinite(mzMinUROI), "mzMin"] }
# mzMax
mzMaxUROI <- unname(vapply(annotationTable(outAnnotation,"mzMax"), max,
na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.infinite(mzMaxUROI)) != 0) {
if (verbose) {
message("uROI max mzMax which are NA are replaced ROI mzMax") }
mzMaxUROI[is.infinite(mzMaxUROI)] <-
outAnnotation@ROI[is.infinite(mzMaxUROI), "mzMax"] }
# store new uROI values
outAnnotation@uROI[, "rtMin"] <- rtMinUROI
outAnnotation@uROI[, "rtMax"] <- rtMaxUROI
outAnnotation@uROI[, "mzMin"] <- mzMinUROI
outAnnotation@uROI[, "mzMax"] <- mzMaxUROI
outAnnotation@uROI[, c("rt", "mz")] <- outAnnotation@ROI[,c("rt", "mz")]
# set uROIExist
outAnnotation@uROIExist <- TRUE
return(outAnnotation)
}
# annotationParamsDiagnostic for FIR
annotationParamsDiagnostic_FIR <- function(outAnnotation, verbose) {
if (verbose) { message('FIR will be calculated as the median of',
' found \"rtMin\",\"rtMax\",\"mzMin\",\"mzMax\"') }
# rtMin
rtMinFIR <- unname(vapply(annotationTable(outAnnotation, "rtMin"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(rtMinFIR)) != 0) {
if (verbose) {
message('FIR median rtMin which are NA are replaced ',
'with uROI rtMin') }
rtMinFIR[is.na(rtMinFIR)] <-
outAnnotation@uROI[is.na(rtMinFIR), "rtMin"] }
# rtMax
rtMaxFIR <- unname(vapply(annotationTable(outAnnotation, "rtMax"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(rtMaxFIR)) != 0) {
if (verbose) {
message('FIR median rtMax which are NA are replaced ',
'with uROI rtMax') }
rtMaxFIR[is.na(rtMaxFIR)] <-
outAnnotation@uROI[is.na(rtMaxFIR), "rtMax"] }
# mzMin
mzMinFIR <- unname(vapply(annotationTable(outAnnotation, "mzMin"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(mzMinFIR)) != 0) {
if (verbose) {
message("FIR median mzMin which are NA are replaced uROI mzMin") }
mzMinFIR[is.na(mzMinFIR)] <-
outAnnotation@uROI[is.na(mzMinFIR), "mzMin"] }
# mzMax
mzMaxFIR <- unname(vapply(annotationTable(outAnnotation, "mzMax"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(mzMaxFIR)) != 0) {
if (verbose) {
message("FIR median mzMax which are NA are replaced uROI mzMax") }
mzMaxFIR[is.na(mzMaxFIR)] <-
outAnnotation@uROI[is.na(mzMaxFIR), "mzMax"] }
# store new FIR values
outAnnotation@FIR[, "rtMin"] <- rtMinFIR
outAnnotation@FIR[, "rtMax"] <- rtMaxFIR
outAnnotation@FIR[, "mzMin"] <- mzMinFIR
outAnnotation@FIR[, "mzMax"] <- mzMaxFIR
return(outAnnotation)
}
## Save annotation parameters as CSV
setGeneric("outputAnnotationParamsCSV",
function(object, saveFolder, verbose = TRUE, noSave=FALSE,...)
standardGeneric("outputAnnotationParamsCSV"))
#' @title Save annotation parameters as CSV
#' @description Save annotation parameters (ROI, uROI and FIR) to disk as a CSV
#' file for editing
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param verbose (bool) If TRUE message progress
#' @param saveFolder (str) Path of folder where annotationParameters_summary.csv
#' will be saved
#' @param noSave (bool) If TRUE the resulting table will be returned without
#' saving to disk
#' @return None
#' @docType methods
#' @aliases outputAnnotationParamsCSV
#' @export
#' @examples
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' spectraPaths <- c('./path/file1', './path/file2', './path/file3')
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' # temporary file
#' savePath <- tempdir()
#'
#' # statistics of an empty annotation
#' outputAnnotationParamsCSV(emptyAnnotation, saveFolder=savePath, verbose=TRUE)
setMethod("outputAnnotationParamsCSV", "peakPantheRAnnotation",
function(object, saveFolder, verbose, noSave) {
# create table
outTable <- data.frame(matrix(, nrow = nbCompounds(object), ncol = 0))
outTable <- cbind(outTable, cpdID = cpdID(object), cpdName=cpdName(object))
# ROI
tmp_ROI <- ROI(object)[, c("rt", "mz", "rtMin", "rtMax", "mzMin", "mzMax")]
colnames(tmp_ROI) <- c("ROI_rt", "ROI_mz", "ROI_rtMin", "ROI_rtMax",
"ROI_mzMin", "ROI_mzMax")
outTable <- cbind(outTable, X = rep("|", nbCompounds(object)), tmp_ROI)
# uROI
tmp_uROI <- uROI(object)[,c("rtMin", "rtMax", "mzMin", "mzMax", "rt", "mz")]
colnames(tmp_uROI) <- c("uROI_rtMin", "uROI_rtMax", "uROI_mzMin",
"uROI_mzMax", "uROI_rt", "uROI_mz")
outTable <- cbind(outTable, X = rep("|", nbCompounds(object)), tmp_uROI)
# FIR
tmp_FIR <- FIR(object)[, c("rtMin", "rtMax", "mzMin", "mzMax")]
colnames(tmp_FIR) <- c("FIR_rtMin", "FIR_rtMax", "FIR_mzMin", "FIR_mzMax")
outTable <- cbind(outTable, X = rep("|", nbCompounds(object)), tmp_FIR)
# save table
if (!noSave){
dir.create(saveFolder, recursive = TRUE, showWarnings = FALSE)
targetFile <- paste(saveFolder, "/annotationParameters_summary.csv",sep="")
if (verbose) {
message("Annotation parameters saved at ", targetFile)
}
utils::write.csv(outTable, file = targetFile, row.names = FALSE,
fileEncoding = "UTF-8")
} else {
return(outTable)
}
})
## Generate fit diagnostic plots
setGeneric("annotationDiagnosticPlots",
function(object, sampleColour = NULL, sampling = 250,
verbose = TRUE, ...)
standardGeneric("annotationDiagnosticPlots"))
#' @title Generate fit diagnostic plots
#' @description Generate fit diagnostic plots for each ROI: \code{EICFit} the
#' raw data and detected feature fit, \code{rtPeakwidthVert} detected peaks
#' retention time apex and peakwidth (vertical and no run order),
#' \code{rtPeakwidthHorzRunOrder} detected peaks retention time apex and
#' peakwidth by run order, \code{mzPeakwidthHorzRunOrder} detected peaks m/z
#' apex and peakwidth by run order, \code{areaRunOrder} detected peaks area by
#' run order, \code{rtHistogram} histogram of detected peaks retention time,
#' \code{mzHistogram} histogram of detected peaks m/z, \code{areaHistogram}
#' histogram of detected peaks area.
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param sampleColour (str) NULL or vector colour for each sample
#' @param sampling (int) Number of points to employ when plotting fittedCurve
#' @param verbose (bool) if TRUE message the plot generation progress
#' @return A list (one list per compound) of diagnostic plots:
#' \code{result[[i]]$EICFit}, \code{result[[i]]$rtPeakwidthVert},
#' \code{result[[i]]$rtPeakwidthHorzRunOrder},
#' \code{result[[i]]$mzPeakwidthHorzRunOrder}, \code{result[[i]]$areaRunOrder},
#' \code{result[[i]]$rtHistogram}, \code{result[[i]]$mzHistogram},
#' \code{result[[i]]$areaHistogram}, \code{result[[i]]$title}
#' @docType methods
#' @aliases annotationDiagnosticPlots
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' annotationDiagnosticPlots(emptyAnnotation)
#' # Warning: the object has not been annotated, return an empty diagnostic plot
#' # list
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' }
setMethod("annotationDiagnosticPlots", "peakPantheRAnnotation",
function(object, sampleColour, sampling, verbose) {
# Init
nbCpd <- nbCompounds(object)
outList <- vector("list", nbCpd)
# Check object was annotated
if (!object@isAnnotated) {
message('Warning: the object has not been annotated, return an',
' empty diagnostic plot list')
return(outList)
}
# Iterate over compounds
for (cpd in seq_len(nbCpd)) {
tmp_annotation <- object[, cpd]
tmp_plotList <- singleDiagnosticPlots(tmp_annotation, sampleColour,
sampling, verbose)
# store results
outList[[cpd]] <- tmp_plotList
if (verbose) {
message("Compound ", cpd, "/", nbCpd, " done")
}
}
return(outList)
})
# diagnostic plots for 1 cpd
singleDiagnosticPlots <- function(tmp_annotation,sampleColour,sampling,verbose){
tmp_plotList <- vector("list", 9)
names(tmp_plotList) <- c("EICFit", "rtPeakwidthVert",
"rtPeakwidthHorzRunOrder", "mzPeakwidthHorzRunOrder","areaRunOrder",
"rtHistogram", "mzHistogram", "areaHistogram", "title")
tmp_plotList$title <- paste(cpdID(tmp_annotation), "-", # title
cpdName(tmp_annotation))
tmp_plotList$EICFit <- peakPantheR_plotEICFit( # plotEICFit
ROIDataPointSampleList = unlist(dataPoints(tmp_annotation),
recursive = FALSE),
curveFitSampleList = unlist(peakFit(tmp_annotation),
recursive = FALSE),
rtMin = annotationTable(tmp_annotation, "rtMin")[, 1],
rtMax = annotationTable(tmp_annotation, "rtMax")[, 1],
sampling = sampling, sampleColour = sampleColour, verbose = verbose)
tmp_plotList$rtPeakwidthVert <- peakPantheR_plotPeakwidth( # RT Pkwidth vert
apexValue = annotationTable(tmp_annotation, "rt")[, 1],
widthMin = annotationTable(tmp_annotation, "rtMin")[, 1],
widthMax = annotationTable(tmp_annotation, "rtMax")[, 1],
acquTime = NULL, sampleColour = sampleColour,
varName = "Retention Time (sec)", rotateAxis=TRUE, verbose=verbose)
tmp_plotList$rtPeakwidthHorzRunOrder <- peakPantheR_plotPeakwidth(#RTPkw hor
apexValue = annotationTable(tmp_annotation, "rt")[, 1],
widthMin = annotationTable(tmp_annotation, "rtMin")[, 1],
widthMax = annotationTable(tmp_annotation, "rtMax")[, 1],
acquTime = acquisitionTime(tmp_annotation),
sampleColour = sampleColour, varName = "Retention Time (sec)",
rotateAxis = FALSE, verbose = verbose)
tmp_plotList$mzPeakwidthHorzRunOrder <- peakPantheR_plotPeakwidth(#MZpkw hor
apexValue = annotationTable(tmp_annotation, "mz")[, 1],
widthMin = annotationTable(tmp_annotation, "mzMin")[, 1],
widthMax = annotationTable(tmp_annotation, "mzMax")[, 1],
acquTime = acquisitionTime(tmp_annotation), sampleColour = sampleColour,
varName = "m/z", rotateAxis = FALSE, verbose = verbose)
tmp_plotList$areaRunOrder <- peakPantheR_plotPeakwidth(# peakarea hor runord
apexValue = annotationTable(tmp_annotation, "peakArea")[, 1],
widthMin = NULL, widthMax = NULL,
acquTime = acquisitionTime(tmp_annotation),
sampleColour = sampleColour, varName = "Peak Area",
rotateAxis = FALSE, verbose = verbose)
tmp_plotList$rtHistogram <- plotHistogram( # RT plotHistogram
var = annotationTable(tmp_annotation, "rt")[, 1],
varName = "Retention Time (sec)", density = TRUE)
tmp_plotList$mzHistogram <- plotHistogram( # mz plotHistogram
var = annotationTable(tmp_annotation, "mz")[, 1],
varName = "m/z", density = TRUE)
tmp_plotList$areaHistogram <- plotHistogram( # peak area plotHistogram
var = annotationTable(tmp_annotation, "peakArea")[, 1],
varName = "Peak Area", density = TRUE)
return(tmp_plotList) }
## Save to disk the annotation parameters as CSV and a diagnostic plot per
## fitted compound
setGeneric("outputAnnotationDiagnostic",
function(object, saveFolder, savePlots = TRUE, sampleColour = NULL,
verbose = TRUE, ncores = 0, ...)
standardGeneric("outputAnnotationDiagnostic"))
#' @title Save to disk the annotation parameters as CSV and a diagnostic plot
#' per fitted compound
#' @description Save to disk the annotation parameters as CSV (as generated by
#' \code{outputAnnotationParamsCSV()}) and a diagnostic plot per fitted compound
#' (as generated by \code{annotationDiagnosticMultiplot()}) if \code{savePlots}
#' is TRUE
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param saveFolder (str) Path of folder where annotationParameters_summary.csv
#' and plots will be saved
#' @param savePlots (bool) If TRUE save a diagnostic plot for each compound
#' @param sampleColour (str) NULL or vector colour for each sample
#' @param verbose (bool) If TRUE message progress
#' @param ncores (int) Number of cores to use to save plots in parallel
#' @param ... Additional parameters for plotting i.e. \code{sampling} for the
#' number of points to employ when plotting fittedCurve
#' @return None
#' @docType methods
#' @aliases outputAnnotationDiagnostic
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' # Calculate annotation
#' annotation <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
#' getAcquTime=FALSE, verbose=FALSE)$annotation
#'
#' # temporary location
#' savePath1 <- tempdir()
#' outputAnnotationDiagnostic(annotation, saveFolder=savePath1, savePlots=FALSE,
#' verbose=TRUE)
#' }
setMethod("outputAnnotationDiagnostic", "peakPantheRAnnotation",
function(object, saveFolder, savePlots, sampleColour, verbose, ncores,...) {
# Save standardised csv
outputAnnotationParamsCSV(object, saveFolder = saveFolder,verbose = verbose)
# Save all fit diagnostic
if (savePlots) {
# iterate over compound (more progressive plot generation and save than
# generating all plots at once)
nbCpd <- nbCompounds(object)
# run in parallel
if (ncores > 0) {
if (verbose) {
message("Saving ", nbCpd, " diagnostic plots in ", saveFolder) }
# Open parallel interface
cl <- parallel::makeCluster(ncores)
doParallel::registerDoParallel(cl)
# Run
savedPlots <- foreach::foreach(x = seq_len(nbCpd),
.inorder = TRUE) %dopar%
outputAnnotationDiagnostic_saveSingleMultiPlot(cpdNb = x,
annotation = object, saveFolder = saveFolder,
sampleColour = sampleColour, nbCpd = nbCpd,
verbose = verbose, ...)
# Close
parallel::stopCluster(cl)
if (verbose) { message("All plots saved") }
# run serial
} else {
if (verbose) { message("Saving diagnostic plots:") }
for (cpd in seq_len(nbCpd)) {
outputAnnotationDiagnostic_saveSingleMultiPlot(cpdNb = cpd,
annotation = object, saveFolder = saveFolder,
sampleColour = sampleColour, nbCpd = nbCpd,
verbose = verbose, ...)
}
}
}
})
# outputAnnotationDiagnostic
outputAnnotationDiagnostic_saveSingleMultiPlot <- function(cpdNb, annotation,
saveFolder, sampleColour, nbCpd, verbose, ...) {
# @param cpdNb (int) cpd number betweem 1 and nbCompounds()
# @param annotation (peakPantheRAnnotation) Annotation object
# @param saveFolder (str) Path where plots will be saved
# @param sampleColour (str) NULL or vector colour for each sample
# @param verbose (bool) message progress
# @param ... Additional parameters for plotting
# subset annotation to only 1 cpd
tmp_annotation <- annotation[, cpdNb]
# diagnostic plots
tmp_diagPlotList <- annotationDiagnosticPlots(tmp_annotation,
sampleColour = sampleColour, verbose = FALSE, ...)
# multiplot
suppressMessages(suppressWarnings(
tmp_multiPlot <- annotationDiagnosticMultiplot(tmp_diagPlotList)))
# save
if (length(tmp_multiPlot) != 0) {
# A4 page size
tmp_targetFile <- paste("cpd_", cpdNb, ".png", sep = "")
ggplot2::ggsave(file = tmp_targetFile, plot = tmp_multiPlot[[1]],
device = "png", path = saveFolder, dpi = 100, width = 21,
height = 29.7, units = "cm", limitsize = FALSE)
grDevices::dev.off()
# output path
if (verbose) {
message(" Compound ", cpdNb, "/", nbCpd,
" diagnostic plot saved at ",
paste(saveFolder, "/", tmp_targetFile, sep = "")) }
# no plot to save
} else {
if (verbose) {
message(" No plot to save for compound ", cpdNb, "/", nbCpd) }
}
return(NA)
}
## Save to disk all annotation results
setGeneric("outputAnnotationResult",
function(object, saveFolder, annotationName = "annotationResult",
verbose = TRUE)
standardGeneric("outputAnnotationResult"))
#' @title Save to disk all annotation results as csv files
#' @description Save to disk all annotation results as
#' \code{annotationName_ ... .csv} files: compound metadata (\code{cpdMetadata},
#' \code{cpdID}, \code{cpdName}) and spectra metadata (\code{spectraMetadata},
#' \code{acquisitionTime}, \code{TIC}), summary of fit (ratio of peaks found:
#' \code{ratio_peaks_found}, ratio of peaks filled: \code{ratio_peaks_filled},
#' mean ppm_error: \code{ppm_error}, mean rt_dev_sec: \code{rt_dev_sec}), and a
#' file for each column of \code{peakTables} (with samples as rows and compounds
#' as columns)
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param saveFolder (str) Path of folder where the annotation result csv will
#' be saved
#' @param annotationName (str) name of annotation to use in the saved csv
#' @param verbose (bool) If TRUE message progress
#' @return None
#' @docType methods
#' @aliases outputAnnotationResult
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' # Calculate annotation
#' annotation <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
#' getAcquTime=FALSE, verbose=FALSE)$annotation
#'
#' # temporary location
#' savePath1 <- tempdir()
#' outputAnnotationResult(annotation, saveFolder=savePath1,
#' annotationName='testProject', verbose=TRUE)
#' }
setMethod("outputAnnotationResult", "peakPantheRAnnotation",
function(object, saveFolder, annotationName, verbose) {
# Check object was annotated
if (!object@isAnnotated) {
stop("Object has not been annotated, no annotation results to save")
}
# Init folder
dir.create(saveFolder, recursive = TRUE, showWarnings = FALSE)
# Save compound metadata
outputAnnotationResult_saveCpdMetadata(object, saveFolder, annotationName,
verbose)
# Save spectra metadata
outputAnnotationResult_saveSpectraMetadata(object, saveFolder,
annotationName, verbose)
# Save peakTables columns
outputAnnotationResult_savePeaktable(object, saveFolder, annotationName,
verbose)
# Save summary table
outputAnnotationResult_saveSummary(object, saveFolder, annotationName,
verbose)
})
# save compound metadata
outputAnnotationResult_saveCpdMetadata <- function(object, saveFolder,
annotationName, verbose) {
tmp_cpdID <- cpdID(object)
tmp_cpdName <- cpdName(object)
tmp_cpdMetadata <- cpdMetadata(object)
# tmp_rt, tmp_mz
nbCpd <- nbCompounds(object)
tmp_rt <- rep(as.numeric(NA), nbCpd)
tmp_mz <- rep(as.numeric(NA), nbCpd)
all_rt <- annotationTable(object, column = "rt")
all_mz <- annotationTable(object, column = "mz")
to_keep <- annotationTable(object, column = "found") &
!annotationTable(object, column = "is_filled")
for (i in seq_len(nbCpd)) {
tmp_rt[i] <- mean(all_rt[to_keep[, i], i])
tmp_mz[i] <- mean(all_mz[to_keep[, i], i])
}
tmp_outCpdMeta <- data.frame(cpdID = tmp_cpdID, cpdName = tmp_cpdName,
rt = tmp_rt, mz = tmp_mz)
colnames(tmp_outCpdMeta) <- c("cpdID", "cpdName", "Retention Time", "m/z")
tmp_outCpdMeta <- cbind(tmp_outCpdMeta, tmp_cpdMetadata)
path_cpdMeta <- paste(saveFolder, "/", annotationName,
"_cpdMetadata.csv", sep = "")
utils::write.csv(tmp_outCpdMeta, file = path_cpdMeta, row.names = FALSE,
fileEncoding = "UTF-8")
if (verbose) { message("Compound metadata saved at ", path_cpdMeta) }
}
# save spectra Metadata
outputAnnotationResult_saveSpectraMetadata <- function(object, saveFolder,
annotationName, verbose) {
tmp_filepath <- filepath(object)
tmp_acqTime <- acquisitionTime(object)
tmp_TIC <- TIC(object)
tmp_spectraMetadata <- spectraMetadata(object)
tmp_outSpecMeta <- data.frame(filepath = tmp_filepath,
acquisitionTime = tmp_acqTime, TIC = tmp_TIC)
tmp_outSpecMeta <- cbind(tmp_outSpecMeta, tmp_spectraMetadata)
path_specMeta <- paste(saveFolder, "/", annotationName,
"_spectraMetadata.csv", sep = "")
utils::write.csv(tmp_outSpecMeta, file = path_specMeta, row.names = FALSE,
fileEncoding = "UTF-8")
if (verbose) { message("Spectra metadata saved at ", path_specMeta) }
}
# save peakTables
outputAnnotationResult_savePeaktable <- function(object, saveFolder,
annotationName, verbose) {
for (i in colnames(object@peakTables[[1]])) {
tmp_var <- annotationTable(object = object, column = i)
path_var <- paste(saveFolder, "/", annotationName, "_", i, ".csv",
sep = "")
utils::write.csv(tmp_var, file = path_var, row.names = TRUE,
fileEncoding = "UTF-8")
if (verbose) {
message("Peak measurement \"", i, "\" saved at ", path_var)
}
}
}
# save summary table
outputAnnotationResult_saveSummary <- function(object, saveFolder,
annotationName, verbose) {
tmp_summary <- data.frame(matrix(ncol = 0, nrow = nbCompounds(object)),
stringsAsFactors = FALSE)
rownames(tmp_summary) <- paste(cpdID(object), "-", cpdName(object))
# used FIR (found = not filled, filled from is_filled)
if (object@useFIR) {
tmp_summary$ratio_peaks_found <- 1 - (colSums(
annotationTable(object, column = "is_filled"))/nbSamples(object))
tmp_summary$ratio_peaks_filled <- (colSums(
annotationTable(object, column = "is_filled"))/nbSamples(object))
# didn't use FIR (found from found, None are filled)
} else {
tmp_summary$ratio_peaks_found <- colSums(
annotationTable(object, column = "found"))/nbSamples(object)
tmp_summary$ratio_peaks_filled <- 0
}
tmp_summary$ppm_error <-
colMeans(annotationTable(object, column = "ppm_error"), na.rm = TRUE)
tmp_summary$rt_dev_sec <-
colMeans(annotationTable(object, column = "rt_dev_sec"), na.rm = TRUE)
path_summary <- paste(saveFolder, "/", annotationName, "_summary.csv",
sep = "")
utils::write.csv(tmp_summary, file = path_summary, row.names = TRUE,
fileEncoding = "UTF-8")
if (verbose) { message("Summary saved at ", path_summary) }
}
#####################################################################
# Reset a peakPantheRAnnotation and alter samples or compounds information
setGeneric("resetAnnotation",
function(previousAnnotation, spectraPaths = NULL, targetFeatTable = NULL,
uROI = NULL, FIR = NULL, cpdMetadata = NULL, spectraMetadata = NULL,
uROIExist = NULL, useUROI = NULL, useFIR = NULL, verbose = TRUE, ...)
standardGeneric("resetAnnotation"))
#' @title Reset a peakPantheRAnnotation and alter samples and compounds
#' information
#' @description Reset a peakPantheRAnnotation (remove results and set
#' \code{isAnnotated=FALSE}). If a different number of samples (
#' \code{spectraPaths}) or compounds (\code{targetFeatTable}) are passed, the
#' object will be initialised to the new size. For input values left as NULL,
#' the slots (\code{filepath} (from \code{spectraPaths}), \code{ROI},
#' \code{cpdID}, \code{cpdName} (from \code{targetFeatTable}), \code{uROI},
#' \code{FIR}, \code{cpdMetadata}, \code{spectraMetadata}, \code{uROIExist},
#' \code{useUROI} and \code{useFIR}) will be filled with values from
#' \code{previousAnnotation}.
#' @param previousAnnotation (peakPantheRAnnotation) object to reset
#' @param spectraPaths NULL or a character vector of spectra file paths, to set
#' samples to process
#' @param targetFeatTable NULL or a \code{\link{data.frame}} of compounds to
#' target as rows and parameters as columns: \code{cpdID} (str), \code{cpdName}
#' (str), \code{rtMin} (float in seconds), \code{rt} (float in seconds, or
#' \emph{NA}), \code{rtMax} (float in seconds), \code{mzMin} (float), \code{mz}
#' (float or \emph{NA}), \code{mzMax} (float). Set compounds to target.
#' @param uROI NULL or a data.frame of updated Regions Of Interest (uROI) with
#' compounds as row and uROI parameters as columns: \code{rtMin} (float in
#' seconds), \code{rt} (float in seconds, or \emph{NA}), \code{rtMax} (float in
#' seconds), \code{mzMin} (float), \code{mz} (float or \emph{NA}), \code{mzMax}
#' (float).
#' @param FIR NULL or a data.frame of Fallback Integration Regions (FIR) with
#' compounds as row and FIR parameters as columns: \code{rtMin} (float in
#' seconds), \code{rtMax} (float in seconds), \code{mzMin} (float), \code{mzMax}
#' (float).
#' @param cpdMetadata NULL or a data.frame of compound metadata, with compounds
#' as row and metadata as columns
#' @param spectraMetadata NULL or a data.frame of sample metadata, with samples
#' as row and metadata as columns
#' @param uROIExist NULL or a logical stating if uROI have been set
#' @param useUROI NULL or a logical stating if uROI are to be used
#' @param useFIR NULL or a logical stating if FIR are to be used
#' @param verbose (bool) If TRUE message progress
#' @param ... Additional slots and values to set when resetting the object
#' (\code{cpdID}, \code{cpdName}, \code{ROI}, \code{filepath}, \code{TIC},
#' \code{acquisitionTime}, \code{peakTables}, \code{dataPoints}, \code{peakFit})
#' @return (peakPantheRAnnotation) object reset with previous results removed
#' and slots updated
#' @docType methods
#' @aliases resetAnnotation
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' smallAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#' smallAnnotation
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 2 samples.
#' # updated ROI do not exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
#'
#' # Reset and change number of spectra
#' newSpectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#' largerAnnotation <- resetAnnotation(smallAnnotation,
#' spectraPaths=newSpectraPaths,
#' verbose=TRUE)
#' largerAnnotation
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 3 samples.
#' # updated ROI do not exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
#' }
setMethod("resetAnnotation", "peakPantheRAnnotation",
function(previousAnnotation, spectraPaths, targetFeatTable, uROI, FIR,
cpdMetadata, spectraMetadata, uROIExist, useUROI, useFIR, verbose, ...){
# If input is NULL, use previousAnnotation value, else use the passed value
# If number of compounds or spectra is changed, the previous values
# (metadata, uROI, FIR) cannot be reused (risk a mismatch of the metadata)
if (verbose) { message("peakPantheRAnnotation object being reset:") }
# targetFeatTable (cpdID, cpdName, ROI), uROI, FIR, cpdMetadata
resetTarg <- resetAnnot_targetFeatTable_uROI_FIR_cpdMeta(previousAnnotation,
targetFeatTable, uROI, FIR, cpdMetadata, verbose)
.targetFeatTable <- resetTarg$target
.uROI <- resetTarg$uROI
.FIR <- resetTarg$FIR
.cpdMetadata <- resetTarg$cpd
# spectraPaths, spectraMetadata
resSpectra <- resetAnnot_spectraPathMetadata(previousAnnotation,
spectraPaths, spectraMetadata, verbose)
.spectraPaths <- resSpectra$spectraPaths
.spectraMetadata <- resSpectra$spectraMetadata
# uROIExist
.uROIExist <- resetAnnot_uROIExist(uROIExist, targetFeatTable,
previousAnnotation, verbose)
# useUROI, useFIR
resUSE <- resetAnnot_useUROIuseFIR(useUROI, useFIR, targetFeatTable,
previousAnnotation, verbose)
.useUROI <- resUSE$useUROI
.useFIR <- resUSE$useFIR
# is annotated
.isAnnotated <- FALSE
# Create new object In all case (old or new value) spectraPaths and
# targetFeatTable will trigger the resetting of all results
peakPantheRAnnotation(spectraPaths = .spectraPaths,
targetFeatTable = .targetFeatTable, uROI = .uROI, FIR = .FIR,
cpdMetadata = .cpdMetadata, spectraMetadata = .spectraMetadata,
uROIExist = .uROIExist, useUROI = .useUROI, useFIR = .useFIR,
isAnnotated = .isAnnotated, ...)
})
# resetAnnotation targetFeatTable (cpdID, cpdName, ROI), uROI, FIR, cpdMetadata
resetAnnot_targetFeatTable_uROI_FIR_cpdMeta <- function(previousAnnotation,
targetFeatTable, uROI, FIR, cpdMetadata, verbose) {
# reuse previous values
if (all(is.null(targetFeatTable))) {
reset <- resetAnnot_prevTargetFeatTable(previousAnnotation, uROI, FIR,
cpdMetadata, verbose)
} else {
# reset to default
reset <- resetAnnot_newTargetFeatTable(targetFeatTable, uROI, FIR,
cpdMetadata, verbose)
}
return(reset)
}
# resetAnnotation reuse previous targetFeatTable
resetAnnot_prevTargetFeatTable <- function(previousAnnotation, uROI, FIR,
cpdMetadata, verbose) {
# previous values
.targetFeatTable <- ROI(previousAnnotation)
if (verbose) {
message(" Previous \"ROI\", \"cpdID\" and \"cpdName\" value kept")
}
# uROI
if (all(is.null(uROI))) { # previous values
.uROI <- uROI(previousAnnotation)[, c("rtMin", "rt", "rtMax",
"mzMin", "mz", "mzMax")]
if (verbose) {
message(" Previous \"uROI\" value kept")
}
} else { # new value
.uROI <- uROI
if (verbose) {
message(" New \"uROI\" value set")
}
}
# FIR
if (all(is.null(FIR))) { # previous values
.FIR <- FIR(previousAnnotation)[, c("rtMin", "rtMax", "mzMin",
"mzMax")]
if (verbose) {
message(" Previous \"FIR\" value kept")
}
} else { # new value
.FIR <- FIR
if (verbose) {
message(" New \"FIR\" value set")
}
}
# cpdMetadata
if (all(is.null(cpdMetadata))) { # previous values
.cpdMetadata <- cpdMetadata(previousAnnotation)
if (verbose) {
message(" Previous \"cpdMetadata\" value kept")
}
} else { # new value
.cpdMetadata <- cpdMetadata
if (verbose) {
message(" New \"cpdMetadata\" value set")
}
}
return(list(target=.targetFeatTable, uROI=.uROI, FIR=.FIR,
cpd=.cpdMetadata))
}
# resetAnnotation new targetFeatTable
resetAnnot_newTargetFeatTable <- function(targetFeatTable, uROI, FIR,
cpdMetadata, verbose) {
# reset to default
.targetFeatTable <- targetFeatTable
if (verbose) {
message(' New \"targetFeatTable\" value set (\"ROI\", ',
'\"cpdID\", \"cpdName\"') }
# uROI
if (all(is.null(uROI))) {
# Do not reuse old values if we change the compounds targeted
.uROI <- data.frame(rtMin = numeric(), rt = numeric(),
rtMax = numeric(), mzMin = numeric(), mz = numeric(),
mzMax = numeric(), stringsAsFactors = FALSE)
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"uROI\" cannot be kept and set to default') }
} else { # new value
.uROI <- uROI
if (verbose) { message(" New \"uROI\" value set") }
}
# FIR
if (all(is.null(FIR))) {
# Do not reuse old values if we change the compounds targeted
.FIR <- data.frame(rtMin = numeric(), rtMax = numeric(),
mzMin = numeric(), mzMax = numeric(), stringsAsFactors = FALSE)
if (verbose) {
message(' Targeted compounds changed, previous \"FIR\"',
' cannot be kept and set to default')
}
} else { # new value
.FIR <- FIR
if (verbose) { message(" New \"FIR\" value set") }
}
# cpdMetadata
if (all(is.null(cpdMetadata))) {
# Do not reuse old values if we change the compounds targeted
.cpdMetadata <- data.frame()
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"cpdMetadata\" cannot be kept and set to default')
}
} else { # new value
.cpdMetadata <- cpdMetadata
if (verbose) { message(" New \"cpdMetadata\" value set") }
}
return(list(target=.targetFeatTable, uROI=.uROI, FIR=.FIR,
cpd=.cpdMetadata))
}
# resetAnnotation spectraPaths, spectraMetadata
resetAnnot_spectraPathMetadata <- function(previousAnnotation, spectraPaths,
spectraMetadata, verbose) {
# reuse previous values
if (all(is.null(spectraPaths))) {
.spectraPaths <- filepath(previousAnnotation)
if (verbose) {
message(" Previous \"filepath\" value kept")
}
# spectraMetadata
if (all(is.null(spectraMetadata))) {
# previous values
.spectraMetadata <- spectraMetadata(previousAnnotation)
if (verbose) {
message(" Previous \"spectraMetadata\" value kept")
}
} else {
# new value
.spectraMetadata <- spectraMetadata
if (verbose) {
message(" New \"spectraMetadata\" value set")
}
}
# new values
} else {
.spectraPaths <- spectraPaths
if (verbose) {
message(" New \"spectraPaths\" value set")
}
# spectraMetadata
if (all(is.null(spectraMetadata))) {
# Do not reuse old values if we change the spectra
.spectraMetadata <- data.frame()
if (verbose) {
message(' Targeted spectra changed, previous ',
'\"spectraMetadata\" cannot be kept and set to default')
}
} else {
# new value
.spectraMetadata <- spectraMetadata
if (verbose) {
message(" New \"spectraMetadata\" value set")
}
}
}
return(list(spectraPaths = .spectraPaths,
spectraMetadata = .spectraMetadata))
}
# resetAnnotation uROIExist
resetAnnot_uROIExist <- function(uROIExist, targetFeatTable, previousAnnotation,
verbose) {
if (all(is.null(uROIExist))) {
# previous values cannot be used if targetFeatTable is changed
if (all(is.null(targetFeatTable))) {
# previous values
.uROIExist <- uROIExist(previousAnnotation)
if (verbose) {
message(" Previous \"uROIExist\" value kept")
}
} else {
# Do not reuse old values if we change the compounds
.uROIExist <- FALSE
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"uROIExist\" cannot be kept and set to default')
}
}
} else {
# new value
.uROIExist <- uROIExist
if (verbose) {
message(" New \"uROIExist\" value set")
}
}
return(.uROIExist)
}
# resetAnnotation useUROI, useFIR
resetAnnot_useUROIuseFIR <- function(useUROI, useFIR, targetFeatTable,
previousAnnotation, verbose){
# useUROI
if (all(is.null(useUROI))) {
# previous values cannot be used if targetFeatTable is changed
if (all(is.null(targetFeatTable))) {
# previous values
.useUROI <- useUROI(previousAnnotation)
if (verbose) {
message(" Previous \"useUROI\" value kept")
}
} else {
# Do not reuse old values if we change the compound
.useUROI <- FALSE
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"useUROI\" cannot be kept and set to default')
}
}
} else { # new value
.useUROI <- useUROI
if (verbose) { message(" New \"useUROI\" value set") }
}
# useFIR
if (all(is.null(useFIR))) {
# previous values cannot be used if targetFeatTable is changed
if (all(is.null(targetFeatTable))) {
# previous values
.useFIR <- useFIR(previousAnnotation)
if (verbose) {
message(" Previous \"useFIR\" value kept")
}
} else { # Do not reuse old values if we change the compound
.useFIR <- FALSE
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"useFIR\" cannot be kept and set to default')
}
}
} else { # new value
.useFIR <- useFIR
if (verbose) { message(" New \"useFIR\" value set") }
}
return(list(useUROI = .useUROI, useFIR = .useFIR))
}
## Reset FIR windows to uROI or ROI values
setGeneric("resetFIR",
function(object, verbose = TRUE, ...)
standardGeneric("resetFIR"))
#' Reset FIR windows to uROI or ROI values
#' Reset FIR windows to uROI (or ROI if \code{uROIExist=FALSE})
#' @param object (peakPantheRAnnotation) object for which FIR are to be reset
#' @param verbose (bool) If TRUE message progress
#' @return (peakPantheRAnnotation) object with FIR values reset
#' @docType methods
#' @aliases resetFIR
#' @export
#' @examples
#' ## Initialise a peakPantheRAnnotation object with 2 targeted compounds
#'
#' ## targetFeatTable
#' input_targetFeatTable <- data.frame(matrix(vector(), 2, 8,
#' dimnames=list(c(), c('cpdID', 'cpdName', 'rtMin',
#' 'rt', 'rtMax', 'mzMin', 'mz', 'mzMax'))),
#' stringsAsFactors=FALSE)
#' input_targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3., 1., 4., 5., 2., 6.)
#' input_targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 19., 17., 20., 21., 18., 22.)
#' input_targetFeatTable[,c(3:8)] <- sapply(input_targetFeatTable[,c(3:8)],
#' as.numeric)
#' ## FIR
#' input_FIR <- data.frame(matrix(vector(), 2, 4, dimnames=list(c(),
#' c('rtMin', 'rtMax', 'mzMin', 'mzMax'))),
#' stringsAsFactors=FALSE)
#' input_FIR[1,] <- c(13., 14., 15., 16.)
#' input_FIR[2,] <- c(29., 30., 31., 32.)
#'
#' annotation <- peakPantheRAnnotation(targetFeatTable = input_targetFeatTable,
#' FIR = input_FIR, uROIExist = FALSE)
#'
#' ## Reset FIR with ROI values as uROI are not set
#' updatedAnnotation <- resetFIR(annotation, verbose=TRUE)
#' # FIR will be reset with ROI values as uROI values are not set
setMethod("resetFIR", "peakPantheRAnnotation",
function(object, verbose) {
# uROI exist
if (uROIExist(object)) {
if (verbose) {
message("FIR will be reset with uROI values")
}
newFIR <- uROI(object)[, c("rtMin", "rtMax", "mzMin", "mzMax")]
# uROI not defined
} else {
if (verbose) {
message('FIR will be reset with ROI values as uROI values ',
'are not set')
}
newFIR <- ROI(object)[, c("rtMin", "rtMax", "mzMin", "mzMax")]
}
object@FIR[, c("rtMin", "rtMax", "mzMin", "mzMax")] <-
newFIR[, c("rtMin", "rtMax", "mzMin", "mzMax")]
return(object)
})
#####################################################################
# Retention time correction: adjust uROI rt based on previously integrated
# signal
setGeneric("retentionTimeCorrection",
function(annotationObject, rtCorrectionReferences=NULL,
method='polynomial', params=list(polynomialOrder=2),
robust=FALSE, rtWindowWidth=15, diagnostic=TRUE)
standardGeneric("retentionTimeCorrection"))
#' @title Apply retention time correction methods to adjust the retention time
#' information in the uROI of peakPantheRAnnotation object
#' @description Performs retention time correction to re-adjust the expected
#' retention time position of compounds.
#' Requires an annotated peakPantheRAnnotation object (\code{isAnnotated=TRUE}).
#' The original \code{rt} value is used as expected and the observed deviation
#' measured in the \code{rt_dev_sec} field is taken as the deviation to be
#' corrected.
#' @param annotationObject (peakPantheRAnnotation) object with previous fit
#' results to adjust retention time values in uROI and FIR
#' annotationObject, rtCorrectionReferences=NULL,
#' @param rtCorrectionReferences (list) of compounds IDs (\code{cpdID})
#' to be used as retention time references.
#' All \code{cpdID} entries must be present in the object and previously
#' annotated. If NULL, use all compounds.
#' @param method (str) name of RT correction method to use (currently
#' \code{polynomial} or \code{constant}
#' @param params (list) list of parameters to pass to each correction method.
#' Currently allowed inputs are \code{polynomialOrder}
#' for \code{method='polynomial'}
#' @param robust (bool) whether to use the RANSAC algorithm to flag and ignore
#' outliers during retention time correction
#' @param rtWindowWidth (numeric) full width in seconds
#' of the retention time window defined around the corrected retention time
#' value for each compound
#' @param diagnostic (bool) If TRUE returns diagnostic plots (specific to each
#' correction method)
#' @return (list) containing entries `annotation`, with the new and retention
#' time corrected peakPantheRAnnotation, and `plot` (if \code{diagnostic=TRUE}).
#' @docType methods
#' @aliases retentionTimeCorrection
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' smallAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#' # annotate files serially
#' annotation_result <- peakPantheR_parallelAnnotation(smallAnnotation,
#' ncores=0, verbose=TRUE)
#' data_annotation <- annotation_result$annotation
#'
#' # Example with constant correction
#' rtCorrectionOutput <- retentionTimeCorrection(
#' annotationObject = data_annotation,
#' rtCorrectionReferences=c('ID-1'),
#' method='constant', params=list(),
#' robust=FALSE,
#' rtWindowWidth=15,
#' diagnostic=TRUE)
#'
#' rtCorrectedAnnotation <- rtCorrectionOutput$annotation
#'
#' # rtCorrectedAnnotation
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 2 samples.
#' # updated ROI exists, with a modified rt (uROI)
#' # uses updated ROI (uROI)
#' # uses fallback integration regions (FIR)
#' # is annotated
#'
#' rtCorrectionPlot <- rtCorrectionOutput$plot
#' # rtCorrectedPlot
#' # A ggplot2 object
#' # Scatterplot where x=`r` in the and y=`rt_dev_sec` from data_annotation
#' # Points colored depending on whether the reference was used to fit
#' # the correction model
#' }
setMethod("retentionTimeCorrection", "peakPantheRAnnotation",
function(annotationObject, rtCorrectionReferences, method, params, robust,
rtWindowWidth, diagnostic) {
newAnnotation <- annotationObject
rtCorrectionReferences <- rtCorrection_checkInput(newAnnotation,
rtCorrectionReferences,rtWindowWidth)
featureInformation <-
rtCorrection_prepareTargetFeatTable(newAnnotation,
rtCorrectionReferences)
referenceTable <- featureInformation$referenceTable
targetFeatTable <- featureInformation$targetFeatTable
newAnnotation <- rtCorrection_prepareAnnotation(newAnnotation,
targetFeatTable, rtWindowWidth)
referenceTable <- referenceTable[!is.na(referenceTable$rt_dev_sec), ]
correctedRtTable <-
peakPantheR_applyRTCorrection(
targetFeatTable[!is.na(targetFeatTable$rt_dev_sec), ],
referenceTable, method,
params, robust)
# Only compounds with measured rt_dev_sec can be adjusted
newAnnotation@uROI[!is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
correctedRtTable$correctedRt - (rtWindowWidth/2)
newAnnotation@uROI[!is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
correctedRtTable$correctedRt + (rtWindowWidth/2)
newAnnotation@uROI[!is.na(targetFeatTable$rt_dev_sec), "rt"] <-
correctedRtTable$correctedRt
newAnnotation@FIR[!is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
correctedRtTable$correctedRt - (rtWindowWidth/2)
newAnnotation@FIR[!is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
correctedRtTable$correctedRt + (rtWindowWidth/2)
if (isTRUE(diagnostic)) {
rtAdjustmentPlot <-
rtCorrection_diagnosticPlot(correctedRtTable)
return(list(annotation=newAnnotation, plot=rtAdjustmentPlot))
} else {return(list(annotation=newAnnotation))}
})
# Helper functions for the retentionTimeCorrection method
rtCorrection_checkInput <- function(annotation, rtCorrectionReferences,
rtWindowWidth) {
if (isFALSE(annotation@isAnnotated)) {
stop(paste('The retention time correction functionality requires an',
'annotated peakPantheRAnnotation object',
'(annotationObject@isAnnotated = TRUE)'))
}
if (is.null(rtCorrectionReferences)) {
rtCorrectionReferences <- annotation@cpdID
} else {
if (!all(rtCorrectionReferences %in% annotation@cpdID)) {
stop(paste('All compound IDs in rtCorrectionReferences must be',
'present on the annotationObject'))
}
}
if (isFALSE(is.numeric(rtWindowWidth)) | rtWindowWidth <= 0) {
stop('rtWindowWidth must be a positive number')
}
return(rtCorrectionReferences)
}
# Helper functions for the retentionTimeCorrection method
rtCorrection_prepareTargetFeatTable <- function(newAnnotation,
rtCorrectionReferences) {
# Obtain the mean retention time deviation per second
rt_dev_secMatrix <- annotationTable(newAnnotation,"rt_dev_sec")
rt_dev_sec_mean <- unname(vapply(rt_dev_secMatrix, mean, na.rm=TRUE,
FUN.VALUE = numeric(1)))
# If uROI exists and useROI was set to true, use that value as original RT,
# otherwise the "theoretical rt" is taken from ROI
if (newAnnotation@uROIExist & newAnnotation@useUROI) {
rt_expected <- newAnnotation@uROI[, "rt"]
} else { rt_expected <- newAnnotation@ROI[, "rt"] }
targetFeatTable <- data.frame(cpdID=newAnnotation@cpdID,
cpdName=newAnnotation@cpdName, rt=rt_expected,
rt_dev_sec=rt_dev_sec_mean)
# subset the references from the table of all compounds to correct
referenceTable <- targetFeatTable[targetFeatTable$cpdID
%in% rtCorrectionReferences, ]
# Exclude features with mean rt_dev_sec = NA from the correction
# function fitting
if (any(is.na(referenceTable$rt_dev_sec))) {
warning(paste("The following references could not be integrated",
"previously and will be excluded:",
referenceTable[is.na(referenceTable$rt_dev_sec), "cpdID"]))
}
if (any(is.na(targetFeatTable$rt_dev_sec))) {
warning(paste("The following compounds could not be",
"integrated previously and will be not be corrected:",
targetFeatTable[is.na(targetFeatTable$rt_dev_sec), "cpdID"]))
}
return(list(targetFeatTable=targetFeatTable,
referenceTable=referenceTable))
}
# Helper functions for the retentionTimeCorrection method
rtCorrection_prepareAnnotation <-function(newAnnotation, targetFeatTable,
rtWindowWidth) {
if (isFALSE(newAnnotation@useUROI)) {
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] <-
newAnnotation@ROI[is.na(targetFeatTable$rt_dev_sec), "rt"]
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] -
(rtWindowWidth/2)
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] +
(rtWindowWidth/2)
newAnnotation@FIR[is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] -
(rtWindowWidth/2)
newAnnotation@FIR[is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] +
(rtWindowWidth/2)
}
# set uROIExist to TRUE
# after corrrection useUROI is TRUE as corrected info is updated there
newAnnotation@uROIExist <- TRUE
newAnnotation@useUROI <- TRUE
return(newAnnotation)
}
rtCorrection_diagnosticPlot <- function(correctedRtTable) {
rtAdjustmentPlot <- ggplot2::ggplot(data=correctedRtTable) +
ggplot2::geom_point(ggplot2::aes(x=rt,
y=rt_dev_sec, col=isReference)) +
ggplot2::geom_line(ggplot2::aes(x=rt,
y=predictedRtDrift))
rtAdjustmentPlot <- rtAdjustmentPlot +
ggplot2::xlab('Retention time') +
ggplot2::ylab('Retention time deviation')
return(rtAdjustmentPlot)
}
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Defines functions rtCorrection_diagnosticPlot rtCorrection_prepareAnnotation rtCorrection_prepareTargetFeatTable rtCorrection_checkInput resetAnnot_useUROIuseFIR resetAnnot_uROIExist resetAnnot_spectraPathMetadata resetAnnot_newTargetFeatTable resetAnnot_prevTargetFeatTable resetAnnot_targetFeatTable_uROI_FIR_cpdMeta outputAnnotationResult_saveSummary outputAnnotationResult_savePeaktable outputAnnotationResult_saveSpectraMetadata outputAnnotationResult_saveCpdMetadata outputAnnotationDiagnostic_saveSingleMultiPlot singleDiagnosticPlots annotationParamsDiagnostic_FIR annotationParamsDiagnostic_uROI subsetting_peakTables_dataPoints_peakFit
#####################################################################
## Constructor for \link{peakPantheRAnnotation-class}, see function
# peakPantheRAnnotation() for the initialisation checks
setMethod("initialize", "peakPantheRAnnotation",
function(.Object, ...) {
## load ... arguments
.Object <- methods::callNextMethod(.Object, ...)
# Check the validity of results
methods::validObject(.Object)
return(.Object)
})
#####################################################################
## show method for \link{peakPantheRAnnotation-class}
setMethod("show",
signature = "peakPantheRAnnotation",
definition = function(object) {
cat("An object of class ", class(object), "\n", sep = "")
cat(" ", length(object@cpdName), " compounds in ",
length(object@filepath), " samples. \n", sep = "")
if (object@uROIExist) {
cat(" updated ROI exist (uROI)\n", sep = "")
} else {
cat(" updated ROI do not exist (uROI)\n", sep = "")
}
if (object@useUROI) {
cat(" uses updated ROI (uROI)\n", sep = "")
} else {
cat(" does not use updated ROI (uROI)\n", sep = "")
}
if (object@useFIR) {
cat(" uses fallback integration regions (FIR)\n", sep = "")
} else {
cat(" does not use fallback integration regions (FIR)\n", sep = "")
}
if (object@isAnnotated) {
cat(" is annotated\n", sep = "")
} else {
cat(" is not annotated\n", sep = "")
}
invisible(NULL)
})
#####################################################################
## validObject method for \link{peakPantheRAnnotation-class}.
# Number of compounds based on @cpdID length, number of samples based on
# @filepath length. Slot type is not checked as \code{setClass} enforces it.
# peakTables, dataPoints and peakFit type are checked on first list element.
setValidity("peakPantheRAnnotation",
function(object) valid_peakPantheRAnnotation(object))
#####################################################################
## Accessors
#####################################################################
# cpdID
setGeneric("cpdID", function(object, ...) standardGeneric("cpdID"))
#' cpdID accessor
#' @param object peakPantheRAnnotation
#' @return (str) A character vector of compound IDs, of length number of
#' compounds
#' @docType methods
#' @aliases cpdID
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin',
#' 'mz', 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' cpdID(annotation)
#' # [1] 'ID-1' 'ID-2'
#' }
setMethod("cpdID", "peakPantheRAnnotation", function(object) {
object@cpdID
})
# cpdName
setGeneric("cpdName", function(object, ...) standardGeneric("cpdName"))
#' cpdName accessor
#' @param object peakPantheRAnnotation
#' @return (str) A character vector of compound names, of length number of
#' compounds
#' @docType methods
#' @aliases cpdName
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' cpdName(annotation)
#' # [1] 'Cpd 1' 'Cpd 2'
#' }
setMethod("cpdName", "peakPantheRAnnotation", function(object) {
object@cpdName
})
# ROI targetFeatTable with ROI
setGeneric("ROI", function(object, ...) standardGeneric("ROI"))
#' ROI accessor returns targetFeatTable with cpdID, cpdName added
#' @param object peakPantheRAnnotation
#' @return (data.frame) target feature table with compounds as row and ROI
#' parameters as columns
#' @docType methods
#' @aliases ROI
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ROI(annotation)
#' # rtMin rt rtMax mzMin mz mzMax cpdID cpdName
#' # 1 3310 3344.888 3390 522.1948 522.2 522.2052 ID-1 Cpd 1
#' # 2 3280 3385.577 3440 496.1950 496.2 496.2050 ID-2 Cpd 2
#' }
setMethod("ROI", "peakPantheRAnnotation", function(object) {
out <- object@ROI
out$cpdID <- object@cpdID
out$cpdName <- object@cpdName
return(out)
})
# uROI targetFeatTable with uROI
setGeneric("uROI", function(object, ...) standardGeneric("uROI"))
#' uROI accessor returns targetFeatTable with cpdID, cpdName added
#' @param object peakPantheRAnnotation
#' @return (data.frame) target feature table with compounds as row and uROI
#' parameters as columns
#' @docType methods
#' @aliases uROI
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' uROI(annotation)
#' # rtMin rt rtMax mzMin mz mzMax cpdID cpdName
#' # 1 NA NA NA NA NA NA ID-1 Cpd 1
#' # 2 NA NA NA NA NA NA ID-2 Cpd 2
#' }
setMethod("uROI", "peakPantheRAnnotation", function(object) {
out <- object@uROI
out$cpdID <- object@cpdID
out$cpdName <- object@cpdName
return(out)
})
# FIR similar to targetFeatTable with FIR
setGeneric("FIR", function(object, ...) standardGeneric("FIR"))
#' FIR accessor returns targetFeatTable with cpdID, cpdName added
#' @param object peakPantheRAnnotation
#' @return (data.frame) target feature table with compounds as row and FIR
#' parameters as columns
#' @docType methods
#' @aliases FIR
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' FIR(annotation)
#' # rtMin rtMax mzMin mzMax cpdID cpdName
#' # 1 NA NA NA NA ID-1 Cpd 1
#' # 2 NA NA NA NA ID-2 Cpd 2
#' }
setMethod("FIR", "peakPantheRAnnotation", function(object) {
out <- object@FIR
out$cpdID <- object@cpdID
out$cpdName <- object@cpdName
return(out)
})
# filepath
setGeneric("filepath", function(object, ...) standardGeneric("filepath"))
#' filepath accessor
#' @param object peakPantheRAnnotation
#' @return (str) A character vector of file paths, of length number of spectra
#' files
#' @docType methods
#' @aliases filepath
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#' filepath(annotation)
#' # [1] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko15.CDF'
#' # [2] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko16.CDF'
#' # [3] 'C:/R/R-3.6.0/library/faahKO/cdf/KO/ko18.CDF'
#' }
setMethod("filepath", "peakPantheRAnnotation", function(object) {
object@filepath
})
# cpdMetadata
setGeneric("cpdMetadata",
function(object, ...) standardGeneric("cpdMetadata"))
#' cpdMetadata accessor
#' @param object peakPantheRAnnotation
#' @return (data.frame) A data.frame of compound metadata, with compounds as row
#' and metadata as columns
#' @docType methods
#' @aliases cpdMetadata
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values not initialised
#' cpdMetadata(annotation)
#' # data frame with 0 columns and 2 rows
#' }
setMethod("cpdMetadata", "peakPantheRAnnotation", function(object) {
object@cpdMetadata
})
# spectraMetadata
setGeneric("spectraMetadata",
function(object, ...) standardGeneric("spectraMetadata"))
#' spectraMetadata accessor
#' @param object peakPantheRAnnotation
#' @return (data.frame) A data.frame of sample metadata, with samples as row and
#' metadata as columns
#' @docType methods
#' @aliases spectraMetadata
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values not initialised
#' spectraMetadata(annotation)
#' # data frame with 0 columns and 3 rows
#' }
setMethod("spectraMetadata", "peakPantheRAnnotation",
function(object) {
object@spectraMetadata
})
# acquisitionTime return converted to POSIXct
setGeneric("acquisitionTime",
function(object, ...) standardGeneric("acquisitionTime"))
#' acquisitionTime accessor returns value as.POSIXct
#' @param object peakPantheRAnnotation
#' @return (POSIXct) A character vector of acquisition date-time (converted from
#' POSIXct) or NA
#' @docType methods
#' @aliases acquisitionTime
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID', 'cpdName', 'rtMin', 'rt', 'rtMax', 'mzMin', 'mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## acquisitionTime can only be extracted from NetCDF files
#' acquisitionTime(annotation)
#' # [1] NA NA NA
#' }
setMethod("acquisitionTime", "peakPantheRAnnotation",
function(object) {
as.POSIXct(object@acquisitionTime)
})
# uROIExist
setGeneric("uROIExist", function(object, ...) standardGeneric("uROIExist"))
#' uROIExist accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if uROI have been set
#' @docType methods
#' @aliases uROIExist
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' uROIExist(annotation)
#' # [1] FALSE
#' }
setMethod("uROIExist", "peakPantheRAnnotation", function(object) {
object@uROIExist
})
# useUROI
setGeneric("useUROI", function(object, ...) standardGeneric("useUROI"))
#' useUROI accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if uROI are to be used
#' @docType methods
#' @aliases useUROI
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' useUROI(annotation)
#' # [1] FALSE
#' }
setMethod("useUROI", "peakPantheRAnnotation", function(object) {
object@useUROI
})
# useFIR
setGeneric("useFIR", function(object, ...) standardGeneric("useFIR"))
#' useFIR accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if FIR are to be used
#' @docType methods
#' @aliases useFIR
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' useFIR(annotation)
#' # [1] FALSE
#' }
setMethod("useFIR", "peakPantheRAnnotation", function(object) {
object@useFIR
})
# TIC
setGeneric("TIC", function(object, ...) standardGeneric("TIC"))
#' TIC accessor
#' @param object peakPantheRAnnotation
#' @return (float) A numeric vector of Total Ion Chromatogram or NA, of length
#' number of spectra files
#' @docType methods
#' @aliases TIC
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' TIC(annotation)
#' # [1] NA NA NA
#' }
setMethod("TIC", "peakPantheRAnnotation", function(object) {
object@TIC
})
# peakTables
setGeneric("peakTables", function(object, ...) standardGeneric("peakTables"))
#' peakTables accessor with cpdID and cpdName added back
#' @param object peakPantheRAnnotation
#' @return (data.frame) A list of peakTable data.frame, of length number of
#' spectra files. Each peakTable data.frame has compounds as rows and peak
#' annotation results as columns, with added compound ID and name.
#' @docType methods
#' @aliases peakTables
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' peakTables(annotation)
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' # [[3]]
#' # NULL
#' }
setMethod("peakTables", "peakPantheRAnnotation", function(object) {
tmpPeakTables <- lapply(object@peakTables, function(x) {
if (!is.null(x)) {
return(cbind.data.frame(x, cpdID = object@cpdID,
cpdName = object@cpdName,
stringsAsFactors = FALSE))
} else {
return(NULL)
}
})
return(tmpPeakTables)
})
# dataPoints
setGeneric("dataPoints", function(object, ...) standardGeneric("dataPoints"))
#' dataPoints accessor
#' @param object peakPantheRAnnotation
#' @return A list of length number of spectra files. Each list element is a
#' \emph{ROIsDataPoint} list of \code{data.frame} of raw data points for each
#' ROI/uROI (retention time 'rt', mass 'mz' and intensity 'int' (as column) of
#' each raw data points (as row))
#' @docType methods
#' @aliases dataPoints
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' dataPoints(annotation)
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' # [[3]]
#' # NULL
#' }
setMethod("dataPoints", "peakPantheRAnnotation", function(object) {
object@dataPoints
})
# peakFit
setGeneric("peakFit", function(object, ...) standardGeneric("peakFit"))
#' peakFit accessor
#' @param object peakPantheRAnnotation
#' @return A list of length number of spectra files. Each list element is a
#' \emph{curveFit} list of \code{peakPantheR_curveFit} or NA for each ROI
#' @docType methods
#' @aliases peakFit
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' peakFit(annotation)
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' # [[3]]
#' # NULL
#' }
setMethod("peakFit", "peakPantheRAnnotation", function(object) {
object@peakFit
})
# isAnnotated
setGeneric("isAnnotated", function(object, ...) standardGeneric("isAnnotated"))
#' isAnnotated accessor
#' @param object peakPantheRAnnotation
#' @return (bool) flag if the annotation has taken place
#' @docType methods
#' @aliases isAnnotated
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' isAnnotated(annotation)
#' # [1] FALSE
#' }
setMethod("isAnnotated", "peakPantheRAnnotation", function(object) {
object@isAnnotated
})
# nbSamples
setGeneric("nbSamples", function(object, ...) standardGeneric("nbSamples"))
#' nbSamples accessor established on filepath
#' @param object peakPantheRAnnotation
#' @return (int) number of samples
#' @docType methods
#' @aliases nbSamples
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' nbSamples(annotation)
#' # [1] 3
#' }
setMethod("nbSamples", "peakPantheRAnnotation", function(object) {
return(length(object@filepath))
})
# nbCompounds
setGeneric("nbCompounds", function(object, ...) standardGeneric("nbCompounds"))
#' nbCompounds accessor established on cpdID
#' @param object peakPantheRAnnotation
#' @return (int) number of samples
#' @docType methods
#' @aliases nbCompounds
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' nbCompounds(annotation)
#' # [1] 2
#' }
setMethod("nbCompounds", "peakPantheRAnnotation", function(object) {
return(length(object@cpdID))
})
# annotationTable
setGeneric("annotationTable",
function(object, column) standardGeneric("annotationTable"))
#' @title annotationTable accessor
#' @description annotationTable returns a dataframe (row samples, col compounds)
#' filled with a specific peakTable column
#' @param object peakPantheRAnnotation
#' @param column a peakTable columns
#' @return (data.frame) (row samples, col compounds) filled with a specific
#' peakTable column
#' @docType methods
#' @aliases annotationTable
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' annotationTable(annotation)
#' # ID-1 ID-2
#' # C:/R/R-3.6.0/library/faahKO/cdf/KO/ko15.CDF NA NA
#' # C:/R/R-3.6.0/library/faahKO/cdf/KO/ko16.CDF NA NA
#' # C:/R/R-3.6.0/library/faahKO/cdf/KO/ko18.CDF NA NA
#' }
setMethod("annotationTable", "peakPantheRAnnotation",
function(object, column) {
## Expect the object to be valid, therefore peakTables is a list of NULL or
## data.frame
nbCpd <- length(object@cpdID)
nbSample <- length(object@filepath)
## Exit with empty data.frame if no samples or only NULL
if (nbSample < 1) {
# an empty data.frame
tmpAnnotation <- data.frame(matrix(vector(), nbSample, nbCpd),
stringsAsFactors = FALSE)
rownames(tmpAnnotation) <- object@filepath
colnames(tmpAnnotation) <- object@cpdID
return(tmpAnnotation)
}
if (is.null(object@peakTables[[1]])) {
# an empty data.frame
tmpAnnotation <- data.frame(matrix(vector(), nbSample, nbCpd),
stringsAsFactors = FALSE)
rownames(tmpAnnotation) <- object@filepath
colnames(tmpAnnotation) <- object@cpdID
return(tmpAnnotation)
}
## Check the column exist
if (!(column %in% colnames(object@peakTables[[1]]))) {
stop("input column is not a column of peakTables")
}
## Concatenate all the results in a single data.frame
tmpAnnotation <- vector("list", nbSample)
for (fl in seq_len(nbSample)) {
tmpAnnotation[fl] <- object@peakTables[[fl]][column]
}
tmpAnnotation <- data.frame(t(do.call("cbind", tmpAnnotation)))
rownames(tmpAnnotation) <- object@filepath
colnames(tmpAnnotation) <- object@cpdID
return(tmpAnnotation)
})
# EICs
setGeneric("EICs",
function(object, aggregationFunction = "sum", ...)
standardGeneric("EICs"))
#' EICs accessor
#' @param object peakPantheRAnnotation
#' @param aggregationFunction (str) Function to use in order to aggregate
#' intensities across mz in each scan. One of \code{sum}, \code{max},
#' \code{min}, \code{mean}
#' @return (float) Extracted Ion Chromatogram aggregated across mz in each scan
#' @docType methods
#' @aliases EICs
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' ## default values without annotation
#' EICs(annotation)
#' # [[1]]
#' # list()
#' # [[2]]
#' # list()
#' # [[3]]
#' # list()
#' }
setMethod("EICs", "peakPantheRAnnotation",
function(object, aggregationFunction) {
tmpEICs <- lapply(object@dataPoints, function(ROIsDataPoint) {
lapply(ROIsDataPoint, function(x) {
generateIonChromatogram(x,aggregationFunction = aggregationFunction)
})
})
return(tmpEICs)
})
# filename
setGeneric("filename", function(object, ...) standardGeneric("filename"))
#' filename accessor by spliting filepath
#' @param object peakPantheRAnnotation
#' @return (str) filename
#' @docType methods
#' @aliases filename
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' filename(annotation)
#' # [1] 'ko15' 'ko16' 'ko18'
#' }
setMethod("filename", "peakPantheRAnnotation", function(object) {
return(tools::file_path_sans_ext(basename(object@filepath)))
})
#####################################################################
# Sub-setting object
#####################################################################
#' extract parts of peakPantheRAnnotation class
#' @param x object from which to extract element(s) or in which to replace
#' element(s).
#' @param i (sample) indices specifying elements to extract or replace
#' @param j (compound) indices specifying elements to extract or replace
#' @param drop not applicable
#' @return (peakPantheRAnnotation) object subset
#'
#' @aliases [,peakPantheRAnnotation-method
#' @docType methods
#'
setMethod("[", "peakPantheRAnnotation",
function(x, i, j, drop = "missing") {
## i is row, samples j is col, compounds
# check inputs and fallback
if (missing(i) & missing(j)) { return(x) }
if (missing(i)) { i <- seq_len(nbSamples(x)) }
if (missing(j)) { j <- seq_len(nbCompounds(x)) }
# check dim size
if (max(i) > nbSamples(x)) {
stop(paste("i index out of bound: maximum", nbSamples(x))) }
if (max(j) > nbCompounds(x)) {
stop(paste("j index out of bound: maximum", nbCompounds(x))) }
# sub-setting
.cpdID <- x@cpdID[j]
.cpdName <- x@cpdName[j]
.ROI <- x@ROI[j, , drop = FALSE]
.FIR <- x@FIR[j, , drop = FALSE]
.uROI <- x@uROI[j, , drop = FALSE]
.filepath <- x@filepath[i]
.cpdMetadata <- x@cpdMetadata[j, , drop = FALSE]
.spectraMetadata <- x@spectraMetadata[i, , drop = FALSE]
.acquisitionTime <- x@acquisitionTime[i]
.uROIExist <- x@uROIExist
.useUROI <- x@useUROI
.useFIR <- x@useFIR
.TIC <- x@TIC[i]
.isAnnotated <- x@isAnnotated
# peakTables, dataPoints & peakFit
subRes <- subsetting_peakTables_dataPoints_peakFit(x, i, j)
.peakTables <- subRes$tmp_peakTables
.dataPoints <- subRes$tmp_dataPoints
.peakFit <- subRes$tmp_peakFit
# load value in new object that will need to pass validObject()
peakPantheRAnnotation(cpdID = .cpdID, cpdName = .cpdName, ROI = .ROI,
FIR = .FIR, uROI = .uROI, filepath = .filepath,
cpdMetadata = .cpdMetadata, spectraMetadata = .spectraMetadata,
acquisitionTime = .acquisitionTime, uROIExist = .uROIExist,
useUROI = .useUROI, useFIR = .useFIR, TIC = .TIC,
peakTables = .peakTables, dataPoints = .dataPoints, peakFit = .peakFit,
isAnnotated = .isAnnotated)
})
# sub-setting peakTables, dataPoints and peakFit
subsetting_peakTables_dataPoints_peakFit <- function(x, i, j) {
# peakTables, filter samples first, then compounds in each table
tmp_peakTables <- x@peakTables[i]
if (all(vapply(tmp_peakTables, is.null, FUN.VALUE = logical(1)))) {
# no cpd filter if all NULL
.peakTables <- tmp_peakTables
} else {
# cpd filter in each table
.peakTables <- lapply(tmp_peakTables, function(x, y) {
x[y, ]
}, y = j)
}
# dataPoints, filter samples first, then compounds in each ROIsDataPoint
tmp_dataPoints <- x@dataPoints[i]
if (all(vapply(tmp_dataPoints, is.null, FUN.VALUE = logical(1)))) {
# no cpd filter if all NULL
.dataPoints <- tmp_dataPoints
} else {
# cpd filter in each ROIsDataPoint
.dataPoints <- lapply(tmp_dataPoints, function(x, y) {
x[y]
}, y = j)
}
# peakFit, filter samples first, then compounds in each curveFit list
tmp_peakFit <- x@peakFit[i]
if (all(vapply(tmp_peakFit, is.null, FUN.VALUE = logical(1)))) {
# no cpd filter if all NULL
.peakFit <- tmp_peakFit
} else {
# cpd filter in each curveFit list
.peakFit <- lapply(tmp_peakFit, function(x, y) {
x[y]
}, y = j)
}
return(list(tmp_peakTables = .peakTables, tmp_dataPoints = .dataPoints,
tmp_peakFit = .peakFit))
}
#####################################################################
## Fit diagnosis
#####################################################################
## Set uROI and FIR based on annotation results
setGeneric("annotationParamsDiagnostic",
function(object, verbose = TRUE, ...)
standardGeneric("annotationParamsDiagnostic"))
#' @title Set uROI and FIR based on annotation results
#' @description Set updated ROI (uROI) and Fallback Integration Regions (FIR)
#' based on the annotation results. If the object is not annotated, it is
#' returned untouched. ROI is not modified. If uROI exist they are left
#' untouched, otherwise they are set as the minimum and maximum found peaks
#' limits (+/-5\% of ROI in retention time). If FIR are used they are left
#' untouched, otherwise they are set as the median of the found limits (rtMin,
#' rtMax, mzMin, mzMax).
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param verbose (bool) If TRUE message progress of uROI and FIR calculation
#' @return (peakPantheRAnnotation) object with updated ROI and FIR set from
#' annotation results
#' @docType methods
#' @aliases annotationParamsDiagnostic
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' annotationParamsDiagnostic(emptyAnnotation, verbose=TRUE)
#' # Warning: the object has not been annotated, return the object untouched
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 3 samples.
#' # updated ROI do not exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
#' }
setMethod("annotationParamsDiagnostic", "peakPantheRAnnotation",
function(object, verbose) {
# init
outAnnotation <- object
# not annotated, pass
if (!outAnnotation@isAnnotated) {
if (verbose) {
message('Warning: the object has not been annotated, return',
' the object untouched') }
return(outAnnotation) }
# uROI uROI doesn't exist, set uROI with min/max of found peaks (if NA, use
# ROI value)
if (!outAnnotation@uROIExist) {
outAnnotation <- annotationParamsDiagnostic_uROI(outAnnotation, verbose)
} else { # uROI exist (even not used), no replacement
if (verbose) { message("uROI already exist, will not be changed") }
}
# FIR FIR not used, recalculate (if NA, use uROI value that was set
# previously)
if (!outAnnotation@useFIR) {
outAnnotation <- annotationParamsDiagnostic_FIR(outAnnotation, verbose)
} else { # FIR used, do not recalculate
if (verbose) { message("FIR in use, will not be changed") }
}
return(outAnnotation)
})
# annotationParamsDiagnostic for uROI
annotationParamsDiagnostic_uROI <- function(outAnnotation, verbose) {
if (verbose) { message('uROI will be set as mimimum/maximum of',
' found peaks (+/-5% of ROI in retention time)') }
# rt ROI 5% (no NA in ROI rtMin/rtMax)
rtMargin <- (ROI(outAnnotation)$rtMax - ROI(outAnnotation)$rtMin) * 0.05
# rtMin (min found peak -5% of ROI)
rtMinUROI <- unname(vapply(annotationTable(outAnnotation,"rtMin"), min,
na.rm = TRUE, FUN.VALUE = numeric(1)))
rtMinUROI <- rtMinUROI - rtMargin
if (sum(is.infinite(rtMinUROI)) != 0) {
if (verbose) { message('uROI min rtMin which are NA are',
' replaced with ROI rtMin') }
rtMinUROI[is.infinite(rtMinUROI)] <-
outAnnotation@ROI[is.infinite(rtMinUROI), "rtMin"] }
# rtMax (max found peak +5% of ROI)
rtMaxUROI <- unname(vapply(annotationTable(outAnnotation,"rtMax"), max,
na.rm = TRUE, FUN.VALUE = numeric(1)))
rtMaxUROI <- rtMaxUROI + rtMargin
if (sum(is.infinite(rtMaxUROI)) != 0) {
if (verbose) { message('uROI max rtMax which are NA are',
' replaced with ROI rtMax') }
rtMaxUROI[is.infinite(rtMaxUROI)] <-
outAnnotation@ROI[is.infinite(rtMaxUROI), "rtMax"] }
# mzMin
mzMinUROI <- unname(vapply(annotationTable(outAnnotation,"mzMin"), min,
na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.infinite(mzMinUROI)) != 0) {
if (verbose) {
message("uROI min mzMin which are NA are replaced ROI mzMin") }
mzMinUROI[is.infinite(mzMinUROI)] <-
outAnnotation@ROI[is.infinite(mzMinUROI), "mzMin"] }
# mzMax
mzMaxUROI <- unname(vapply(annotationTable(outAnnotation,"mzMax"), max,
na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.infinite(mzMaxUROI)) != 0) {
if (verbose) {
message("uROI max mzMax which are NA are replaced ROI mzMax") }
mzMaxUROI[is.infinite(mzMaxUROI)] <-
outAnnotation@ROI[is.infinite(mzMaxUROI), "mzMax"] }
# store new uROI values
outAnnotation@uROI[, "rtMin"] <- rtMinUROI
outAnnotation@uROI[, "rtMax"] <- rtMaxUROI
outAnnotation@uROI[, "mzMin"] <- mzMinUROI
outAnnotation@uROI[, "mzMax"] <- mzMaxUROI
outAnnotation@uROI[, c("rt", "mz")] <- outAnnotation@ROI[,c("rt", "mz")]
# set uROIExist
outAnnotation@uROIExist <- TRUE
return(outAnnotation)
}
# annotationParamsDiagnostic for FIR
annotationParamsDiagnostic_FIR <- function(outAnnotation, verbose) {
if (verbose) { message('FIR will be calculated as the median of',
' found \"rtMin\",\"rtMax\",\"mzMin\",\"mzMax\"') }
# rtMin
rtMinFIR <- unname(vapply(annotationTable(outAnnotation, "rtMin"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(rtMinFIR)) != 0) {
if (verbose) {
message('FIR median rtMin which are NA are replaced ',
'with uROI rtMin') }
rtMinFIR[is.na(rtMinFIR)] <-
outAnnotation@uROI[is.na(rtMinFIR), "rtMin"] }
# rtMax
rtMaxFIR <- unname(vapply(annotationTable(outAnnotation, "rtMax"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(rtMaxFIR)) != 0) {
if (verbose) {
message('FIR median rtMax which are NA are replaced ',
'with uROI rtMax') }
rtMaxFIR[is.na(rtMaxFIR)] <-
outAnnotation@uROI[is.na(rtMaxFIR), "rtMax"] }
# mzMin
mzMinFIR <- unname(vapply(annotationTable(outAnnotation, "mzMin"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(mzMinFIR)) != 0) {
if (verbose) {
message("FIR median mzMin which are NA are replaced uROI mzMin") }
mzMinFIR[is.na(mzMinFIR)] <-
outAnnotation@uROI[is.na(mzMinFIR), "mzMin"] }
# mzMax
mzMaxFIR <- unname(vapply(annotationTable(outAnnotation, "mzMax"),
stats::median, na.rm = TRUE, FUN.VALUE = numeric(1)))
if (sum(is.na(mzMaxFIR)) != 0) {
if (verbose) {
message("FIR median mzMax which are NA are replaced uROI mzMax") }
mzMaxFIR[is.na(mzMaxFIR)] <-
outAnnotation@uROI[is.na(mzMaxFIR), "mzMax"] }
# store new FIR values
outAnnotation@FIR[, "rtMin"] <- rtMinFIR
outAnnotation@FIR[, "rtMax"] <- rtMaxFIR
outAnnotation@FIR[, "mzMin"] <- mzMinFIR
outAnnotation@FIR[, "mzMax"] <- mzMaxFIR
return(outAnnotation)
}
## Save annotation parameters as CSV
setGeneric("outputAnnotationParamsCSV",
function(object, saveFolder, verbose = TRUE, noSave=FALSE,...)
standardGeneric("outputAnnotationParamsCSV"))
#' @title Save annotation parameters as CSV
#' @description Save annotation parameters (ROI, uROI and FIR) to disk as a CSV
#' file for editing
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param verbose (bool) If TRUE message progress
#' @param saveFolder (str) Path of folder where annotationParameters_summary.csv
#' will be saved
#' @param noSave (bool) If TRUE the resulting table will be returned without
#' saving to disk
#' @return None
#' @docType methods
#' @aliases outputAnnotationParamsCSV
#' @export
#' @examples
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' spectraPaths <- c('./path/file1', './path/file2', './path/file3')
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' # temporary file
#' savePath <- tempdir()
#'
#' # statistics of an empty annotation
#' outputAnnotationParamsCSV(emptyAnnotation, saveFolder=savePath, verbose=TRUE)
setMethod("outputAnnotationParamsCSV", "peakPantheRAnnotation",
function(object, saveFolder, verbose, noSave) {
# create table
outTable <- data.frame(matrix(, nrow = nbCompounds(object), ncol = 0))
outTable <- cbind(outTable, cpdID = cpdID(object), cpdName=cpdName(object))
# ROI
tmp_ROI <- ROI(object)[, c("rt", "mz", "rtMin", "rtMax", "mzMin", "mzMax")]
colnames(tmp_ROI) <- c("ROI_rt", "ROI_mz", "ROI_rtMin", "ROI_rtMax",
"ROI_mzMin", "ROI_mzMax")
outTable <- cbind(outTable, X = rep("|", nbCompounds(object)), tmp_ROI)
# uROI
tmp_uROI <- uROI(object)[,c("rtMin", "rtMax", "mzMin", "mzMax", "rt", "mz")]
colnames(tmp_uROI) <- c("uROI_rtMin", "uROI_rtMax", "uROI_mzMin",
"uROI_mzMax", "uROI_rt", "uROI_mz")
outTable <- cbind(outTable, X = rep("|", nbCompounds(object)), tmp_uROI)
# FIR
tmp_FIR <- FIR(object)[, c("rtMin", "rtMax", "mzMin", "mzMax")]
colnames(tmp_FIR) <- c("FIR_rtMin", "FIR_rtMax", "FIR_mzMin", "FIR_mzMax")
outTable <- cbind(outTable, X = rep("|", nbCompounds(object)), tmp_FIR)
# save table
if (!noSave){
dir.create(saveFolder, recursive = TRUE, showWarnings = FALSE)
targetFile <- paste(saveFolder, "/annotationParameters_summary.csv",sep="")
if (verbose) {
message("Annotation parameters saved at ", targetFile)
}
utils::write.csv(outTable, file = targetFile, row.names = FALSE,
fileEncoding = "UTF-8")
} else {
return(outTable)
}
})
## Generate fit diagnostic plots
setGeneric("annotationDiagnosticPlots",
function(object, sampleColour = NULL, sampling = 250,
verbose = TRUE, ...)
standardGeneric("annotationDiagnosticPlots"))
#' @title Generate fit diagnostic plots
#' @description Generate fit diagnostic plots for each ROI: \code{EICFit} the
#' raw data and detected feature fit, \code{rtPeakwidthVert} detected peaks
#' retention time apex and peakwidth (vertical and no run order),
#' \code{rtPeakwidthHorzRunOrder} detected peaks retention time apex and
#' peakwidth by run order, \code{mzPeakwidthHorzRunOrder} detected peaks m/z
#' apex and peakwidth by run order, \code{areaRunOrder} detected peaks area by
#' run order, \code{rtHistogram} histogram of detected peaks retention time,
#' \code{mzHistogram} histogram of detected peaks m/z, \code{areaHistogram}
#' histogram of detected peaks area.
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param sampleColour (str) NULL or vector colour for each sample
#' @param sampling (int) Number of points to employ when plotting fittedCurve
#' @param verbose (bool) if TRUE message the plot generation progress
#' @return A list (one list per compound) of diagnostic plots:
#' \code{result[[i]]$EICFit}, \code{result[[i]]$rtPeakwidthVert},
#' \code{result[[i]]$rtPeakwidthHorzRunOrder},
#' \code{result[[i]]$mzPeakwidthHorzRunOrder}, \code{result[[i]]$areaRunOrder},
#' \code{result[[i]]$rtHistogram}, \code{result[[i]]$mzHistogram},
#' \code{result[[i]]$areaHistogram}, \code{result[[i]]$title}
#' @docType methods
#' @aliases annotationDiagnosticPlots
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' annotationDiagnosticPlots(emptyAnnotation)
#' # Warning: the object has not been annotated, return an empty diagnostic plot
#' # list
#' # [[1]]
#' # NULL
#' # [[2]]
#' # NULL
#' }
setMethod("annotationDiagnosticPlots", "peakPantheRAnnotation",
function(object, sampleColour, sampling, verbose) {
# Init
nbCpd <- nbCompounds(object)
outList <- vector("list", nbCpd)
# Check object was annotated
if (!object@isAnnotated) {
message('Warning: the object has not been annotated, return an',
' empty diagnostic plot list')
return(outList)
}
# Iterate over compounds
for (cpd in seq_len(nbCpd)) {
tmp_annotation <- object[, cpd]
tmp_plotList <- singleDiagnosticPlots(tmp_annotation, sampleColour,
sampling, verbose)
# store results
outList[[cpd]] <- tmp_plotList
if (verbose) {
message("Compound ", cpd, "/", nbCpd, " done")
}
}
return(outList)
})
# diagnostic plots for 1 cpd
singleDiagnosticPlots <- function(tmp_annotation,sampleColour,sampling,verbose){
tmp_plotList <- vector("list", 9)
names(tmp_plotList) <- c("EICFit", "rtPeakwidthVert",
"rtPeakwidthHorzRunOrder", "mzPeakwidthHorzRunOrder","areaRunOrder",
"rtHistogram", "mzHistogram", "areaHistogram", "title")
tmp_plotList$title <- paste(cpdID(tmp_annotation), "-", # title
cpdName(tmp_annotation))
tmp_plotList$EICFit <- peakPantheR_plotEICFit( # plotEICFit
ROIDataPointSampleList = unlist(dataPoints(tmp_annotation),
recursive = FALSE),
curveFitSampleList = unlist(peakFit(tmp_annotation),
recursive = FALSE),
rtMin = annotationTable(tmp_annotation, "rtMin")[, 1],
rtMax = annotationTable(tmp_annotation, "rtMax")[, 1],
sampling = sampling, sampleColour = sampleColour, verbose = verbose)
tmp_plotList$rtPeakwidthVert <- peakPantheR_plotPeakwidth( # RT Pkwidth vert
apexValue = annotationTable(tmp_annotation, "rt")[, 1],
widthMin = annotationTable(tmp_annotation, "rtMin")[, 1],
widthMax = annotationTable(tmp_annotation, "rtMax")[, 1],
acquTime = NULL, sampleColour = sampleColour,
varName = "Retention Time (sec)", rotateAxis=TRUE, verbose=verbose)
tmp_plotList$rtPeakwidthHorzRunOrder <- peakPantheR_plotPeakwidth(#RTPkw hor
apexValue = annotationTable(tmp_annotation, "rt")[, 1],
widthMin = annotationTable(tmp_annotation, "rtMin")[, 1],
widthMax = annotationTable(tmp_annotation, "rtMax")[, 1],
acquTime = acquisitionTime(tmp_annotation),
sampleColour = sampleColour, varName = "Retention Time (sec)",
rotateAxis = FALSE, verbose = verbose)
tmp_plotList$mzPeakwidthHorzRunOrder <- peakPantheR_plotPeakwidth(#MZpkw hor
apexValue = annotationTable(tmp_annotation, "mz")[, 1],
widthMin = annotationTable(tmp_annotation, "mzMin")[, 1],
widthMax = annotationTable(tmp_annotation, "mzMax")[, 1],
acquTime = acquisitionTime(tmp_annotation), sampleColour = sampleColour,
varName = "m/z", rotateAxis = FALSE, verbose = verbose)
tmp_plotList$areaRunOrder <- peakPantheR_plotPeakwidth(# peakarea hor runord
apexValue = annotationTable(tmp_annotation, "peakArea")[, 1],
widthMin = NULL, widthMax = NULL,
acquTime = acquisitionTime(tmp_annotation),
sampleColour = sampleColour, varName = "Peak Area",
rotateAxis = FALSE, verbose = verbose)
tmp_plotList$rtHistogram <- plotHistogram( # RT plotHistogram
var = annotationTable(tmp_annotation, "rt")[, 1],
varName = "Retention Time (sec)", density = TRUE)
tmp_plotList$mzHistogram <- plotHistogram( # mz plotHistogram
var = annotationTable(tmp_annotation, "mz")[, 1],
varName = "m/z", density = TRUE)
tmp_plotList$areaHistogram <- plotHistogram( # peak area plotHistogram
var = annotationTable(tmp_annotation, "peakArea")[, 1],
varName = "Peak Area", density = TRUE)
return(tmp_plotList) }
## Save to disk the annotation parameters as CSV and a diagnostic plot per
## fitted compound
setGeneric("outputAnnotationDiagnostic",
function(object, saveFolder, savePlots = TRUE, sampleColour = NULL,
verbose = TRUE, ncores = 0, ...)
standardGeneric("outputAnnotationDiagnostic"))
#' @title Save to disk the annotation parameters as CSV and a diagnostic plot
#' per fitted compound
#' @description Save to disk the annotation parameters as CSV (as generated by
#' \code{outputAnnotationParamsCSV()}) and a diagnostic plot per fitted compound
#' (as generated by \code{annotationDiagnosticMultiplot()}) if \code{savePlots}
#' is TRUE
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param saveFolder (str) Path of folder where annotationParameters_summary.csv
#' and plots will be saved
#' @param savePlots (bool) If TRUE save a diagnostic plot for each compound
#' @param sampleColour (str) NULL or vector colour for each sample
#' @param verbose (bool) If TRUE message progress
#' @param ncores (int) Number of cores to use to save plots in parallel
#' @param ... Additional parameters for plotting i.e. \code{sampling} for the
#' number of points to employ when plotting fittedCurve
#' @return None
#' @docType methods
#' @aliases outputAnnotationDiagnostic
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' # Calculate annotation
#' annotation <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
#' getAcquTime=FALSE, verbose=FALSE)$annotation
#'
#' # temporary location
#' savePath1 <- tempdir()
#' outputAnnotationDiagnostic(annotation, saveFolder=savePath1, savePlots=FALSE,
#' verbose=TRUE)
#' }
setMethod("outputAnnotationDiagnostic", "peakPantheRAnnotation",
function(object, saveFolder, savePlots, sampleColour, verbose, ncores,...) {
# Save standardised csv
outputAnnotationParamsCSV(object, saveFolder = saveFolder,verbose = verbose)
# Save all fit diagnostic
if (savePlots) {
# iterate over compound (more progressive plot generation and save than
# generating all plots at once)
nbCpd <- nbCompounds(object)
# run in parallel
if (ncores > 0) {
if (verbose) {
message("Saving ", nbCpd, " diagnostic plots in ", saveFolder) }
# Open parallel interface
cl <- parallel::makeCluster(ncores)
doParallel::registerDoParallel(cl)
# Run
savedPlots <- foreach::foreach(x = seq_len(nbCpd),
.inorder = TRUE) %dopar%
outputAnnotationDiagnostic_saveSingleMultiPlot(cpdNb = x,
annotation = object, saveFolder = saveFolder,
sampleColour = sampleColour, nbCpd = nbCpd,
verbose = verbose, ...)
# Close
parallel::stopCluster(cl)
if (verbose) { message("All plots saved") }
# run serial
} else {
if (verbose) { message("Saving diagnostic plots:") }
for (cpd in seq_len(nbCpd)) {
outputAnnotationDiagnostic_saveSingleMultiPlot(cpdNb = cpd,
annotation = object, saveFolder = saveFolder,
sampleColour = sampleColour, nbCpd = nbCpd,
verbose = verbose, ...)
}
}
}
})
# outputAnnotationDiagnostic
outputAnnotationDiagnostic_saveSingleMultiPlot <- function(cpdNb, annotation,
saveFolder, sampleColour, nbCpd, verbose, ...) {
# @param cpdNb (int) cpd number betweem 1 and nbCompounds()
# @param annotation (peakPantheRAnnotation) Annotation object
# @param saveFolder (str) Path where plots will be saved
# @param sampleColour (str) NULL or vector colour for each sample
# @param verbose (bool) message progress
# @param ... Additional parameters for plotting
# subset annotation to only 1 cpd
tmp_annotation <- annotation[, cpdNb]
# diagnostic plots
tmp_diagPlotList <- annotationDiagnosticPlots(tmp_annotation,
sampleColour = sampleColour, verbose = FALSE, ...)
# multiplot
suppressMessages(suppressWarnings(
tmp_multiPlot <- annotationDiagnosticMultiplot(tmp_diagPlotList)))
# save
if (length(tmp_multiPlot) != 0) {
# A4 page size
tmp_targetFile <- paste("cpd_", cpdNb, ".png", sep = "")
ggplot2::ggsave(file = tmp_targetFile, plot = tmp_multiPlot[[1]],
device = "png", path = saveFolder, dpi = 100, width = 21,
height = 29.7, units = "cm", limitsize = FALSE)
grDevices::dev.off()
# output path
if (verbose) {
message(" Compound ", cpdNb, "/", nbCpd,
" diagnostic plot saved at ",
paste(saveFolder, "/", tmp_targetFile, sep = "")) }
# no plot to save
} else {
if (verbose) {
message(" No plot to save for compound ", cpdNb, "/", nbCpd) }
}
return(NA)
}
## Save to disk all annotation results
setGeneric("outputAnnotationResult",
function(object, saveFolder, annotationName = "annotationResult",
verbose = TRUE)
standardGeneric("outputAnnotationResult"))
#' @title Save to disk all annotation results as csv files
#' @description Save to disk all annotation results as
#' \code{annotationName_ ... .csv} files: compound metadata (\code{cpdMetadata},
#' \code{cpdID}, \code{cpdName}) and spectra metadata (\code{spectraMetadata},
#' \code{acquisitionTime}, \code{TIC}), summary of fit (ratio of peaks found:
#' \code{ratio_peaks_found}, ratio of peaks filled: \code{ratio_peaks_filled},
#' mean ppm_error: \code{ppm_error}, mean rt_dev_sec: \code{rt_dev_sec}), and a
#' file for each column of \code{peakTables} (with samples as rows and compounds
#' as columns)
#' @param object (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
#' @param saveFolder (str) Path of folder where the annotation result csv will
#' be saved
#' @param annotationName (str) name of annotation to use in the saved csv
#' @param verbose (bool) If TRUE message progress
#' @return None
#' @docType methods
#' @aliases outputAnnotationResult
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#'
#' # Calculate annotation
#' annotation <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
#' getAcquTime=FALSE, verbose=FALSE)$annotation
#'
#' # temporary location
#' savePath1 <- tempdir()
#' outputAnnotationResult(annotation, saveFolder=savePath1,
#' annotationName='testProject', verbose=TRUE)
#' }
setMethod("outputAnnotationResult", "peakPantheRAnnotation",
function(object, saveFolder, annotationName, verbose) {
# Check object was annotated
if (!object@isAnnotated) {
stop("Object has not been annotated, no annotation results to save")
}
# Init folder
dir.create(saveFolder, recursive = TRUE, showWarnings = FALSE)
# Save compound metadata
outputAnnotationResult_saveCpdMetadata(object, saveFolder, annotationName,
verbose)
# Save spectra metadata
outputAnnotationResult_saveSpectraMetadata(object, saveFolder,
annotationName, verbose)
# Save peakTables columns
outputAnnotationResult_savePeaktable(object, saveFolder, annotationName,
verbose)
# Save summary table
outputAnnotationResult_saveSummary(object, saveFolder, annotationName,
verbose)
})
# save compound metadata
outputAnnotationResult_saveCpdMetadata <- function(object, saveFolder,
annotationName, verbose) {
tmp_cpdID <- cpdID(object)
tmp_cpdName <- cpdName(object)
tmp_cpdMetadata <- cpdMetadata(object)
# tmp_rt, tmp_mz
nbCpd <- nbCompounds(object)
tmp_rt <- rep(as.numeric(NA), nbCpd)
tmp_mz <- rep(as.numeric(NA), nbCpd)
all_rt <- annotationTable(object, column = "rt")
all_mz <- annotationTable(object, column = "mz")
to_keep <- annotationTable(object, column = "found") &
!annotationTable(object, column = "is_filled")
for (i in seq_len(nbCpd)) {
tmp_rt[i] <- mean(all_rt[to_keep[, i], i])
tmp_mz[i] <- mean(all_mz[to_keep[, i], i])
}
tmp_outCpdMeta <- data.frame(cpdID = tmp_cpdID, cpdName = tmp_cpdName,
rt = tmp_rt, mz = tmp_mz)
colnames(tmp_outCpdMeta) <- c("cpdID", "cpdName", "Retention Time", "m/z")
tmp_outCpdMeta <- cbind(tmp_outCpdMeta, tmp_cpdMetadata)
path_cpdMeta <- paste(saveFolder, "/", annotationName,
"_cpdMetadata.csv", sep = "")
utils::write.csv(tmp_outCpdMeta, file = path_cpdMeta, row.names = FALSE,
fileEncoding = "UTF-8")
if (verbose) { message("Compound metadata saved at ", path_cpdMeta) }
}
# save spectra Metadata
outputAnnotationResult_saveSpectraMetadata <- function(object, saveFolder,
annotationName, verbose) {
tmp_filepath <- filepath(object)
tmp_acqTime <- acquisitionTime(object)
tmp_TIC <- TIC(object)
tmp_spectraMetadata <- spectraMetadata(object)
tmp_outSpecMeta <- data.frame(filepath = tmp_filepath,
acquisitionTime = tmp_acqTime, TIC = tmp_TIC)
tmp_outSpecMeta <- cbind(tmp_outSpecMeta, tmp_spectraMetadata)
path_specMeta <- paste(saveFolder, "/", annotationName,
"_spectraMetadata.csv", sep = "")
utils::write.csv(tmp_outSpecMeta, file = path_specMeta, row.names = FALSE,
fileEncoding = "UTF-8")
if (verbose) { message("Spectra metadata saved at ", path_specMeta) }
}
# save peakTables
outputAnnotationResult_savePeaktable <- function(object, saveFolder,
annotationName, verbose) {
for (i in colnames(object@peakTables[[1]])) {
tmp_var <- annotationTable(object = object, column = i)
path_var <- paste(saveFolder, "/", annotationName, "_", i, ".csv",
sep = "")
utils::write.csv(tmp_var, file = path_var, row.names = TRUE,
fileEncoding = "UTF-8")
if (verbose) {
message("Peak measurement \"", i, "\" saved at ", path_var)
}
}
}
# save summary table
outputAnnotationResult_saveSummary <- function(object, saveFolder,
annotationName, verbose) {
tmp_summary <- data.frame(matrix(ncol = 0, nrow = nbCompounds(object)),
stringsAsFactors = FALSE)
rownames(tmp_summary) <- paste(cpdID(object), "-", cpdName(object))
# used FIR (found = not filled, filled from is_filled)
if (object@useFIR) {
tmp_summary$ratio_peaks_found <- 1 - (colSums(
annotationTable(object, column = "is_filled"))/nbSamples(object))
tmp_summary$ratio_peaks_filled <- (colSums(
annotationTable(object, column = "is_filled"))/nbSamples(object))
# didn't use FIR (found from found, None are filled)
} else {
tmp_summary$ratio_peaks_found <- colSums(
annotationTable(object, column = "found"))/nbSamples(object)
tmp_summary$ratio_peaks_filled <- 0
}
tmp_summary$ppm_error <-
colMeans(annotationTable(object, column = "ppm_error"), na.rm = TRUE)
tmp_summary$rt_dev_sec <-
colMeans(annotationTable(object, column = "rt_dev_sec"), na.rm = TRUE)
path_summary <- paste(saveFolder, "/", annotationName, "_summary.csv",
sep = "")
utils::write.csv(tmp_summary, file = path_summary, row.names = TRUE,
fileEncoding = "UTF-8")
if (verbose) { message("Summary saved at ", path_summary) }
}
#####################################################################
# Reset a peakPantheRAnnotation and alter samples or compounds information
setGeneric("resetAnnotation",
function(previousAnnotation, spectraPaths = NULL, targetFeatTable = NULL,
uROI = NULL, FIR = NULL, cpdMetadata = NULL, spectraMetadata = NULL,
uROIExist = NULL, useUROI = NULL, useFIR = NULL, verbose = TRUE, ...)
standardGeneric("resetAnnotation"))
#' @title Reset a peakPantheRAnnotation and alter samples and compounds
#' information
#' @description Reset a peakPantheRAnnotation (remove results and set
#' \code{isAnnotated=FALSE}). If a different number of samples (
#' \code{spectraPaths}) or compounds (\code{targetFeatTable}) are passed, the
#' object will be initialised to the new size. For input values left as NULL,
#' the slots (\code{filepath} (from \code{spectraPaths}), \code{ROI},
#' \code{cpdID}, \code{cpdName} (from \code{targetFeatTable}), \code{uROI},
#' \code{FIR}, \code{cpdMetadata}, \code{spectraMetadata}, \code{uROIExist},
#' \code{useUROI} and \code{useFIR}) will be filled with values from
#' \code{previousAnnotation}.
#' @param previousAnnotation (peakPantheRAnnotation) object to reset
#' @param spectraPaths NULL or a character vector of spectra file paths, to set
#' samples to process
#' @param targetFeatTable NULL or a \code{\link{data.frame}} of compounds to
#' target as rows and parameters as columns: \code{cpdID} (str), \code{cpdName}
#' (str), \code{rtMin} (float in seconds), \code{rt} (float in seconds, or
#' \emph{NA}), \code{rtMax} (float in seconds), \code{mzMin} (float), \code{mz}
#' (float or \emph{NA}), \code{mzMax} (float). Set compounds to target.
#' @param uROI NULL or a data.frame of updated Regions Of Interest (uROI) with
#' compounds as row and uROI parameters as columns: \code{rtMin} (float in
#' seconds), \code{rt} (float in seconds, or \emph{NA}), \code{rtMax} (float in
#' seconds), \code{mzMin} (float), \code{mz} (float or \emph{NA}), \code{mzMax}
#' (float).
#' @param FIR NULL or a data.frame of Fallback Integration Regions (FIR) with
#' compounds as row and FIR parameters as columns: \code{rtMin} (float in
#' seconds), \code{rtMax} (float in seconds), \code{mzMin} (float), \code{mzMax}
#' (float).
#' @param cpdMetadata NULL or a data.frame of compound metadata, with compounds
#' as row and metadata as columns
#' @param spectraMetadata NULL or a data.frame of sample metadata, with samples
#' as row and metadata as columns
#' @param uROIExist NULL or a logical stating if uROI have been set
#' @param useUROI NULL or a logical stating if uROI are to be used
#' @param useFIR NULL or a logical stating if FIR are to be used
#' @param verbose (bool) If TRUE message progress
#' @param ... Additional slots and values to set when resetting the object
#' (\code{cpdID}, \code{cpdName}, \code{ROI}, \code{filepath}, \code{TIC},
#' \code{acquisitionTime}, \code{peakTables}, \code{dataPoints}, \code{peakFit})
#' @return (peakPantheRAnnotation) object reset with previous results removed
#' and slots updated
#' @docType methods
#' @aliases resetAnnotation
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' smallAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#' smallAnnotation
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 2 samples.
#' # updated ROI do not exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
#'
#' # Reset and change number of spectra
#' newSpectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko18.CDF', package = 'faahKO'))
#' largerAnnotation <- resetAnnotation(smallAnnotation,
#' spectraPaths=newSpectraPaths,
#' verbose=TRUE)
#' largerAnnotation
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 3 samples.
#' # updated ROI do not exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
#' }
setMethod("resetAnnotation", "peakPantheRAnnotation",
function(previousAnnotation, spectraPaths, targetFeatTable, uROI, FIR,
cpdMetadata, spectraMetadata, uROIExist, useUROI, useFIR, verbose, ...){
# If input is NULL, use previousAnnotation value, else use the passed value
# If number of compounds or spectra is changed, the previous values
# (metadata, uROI, FIR) cannot be reused (risk a mismatch of the metadata)
if (verbose) { message("peakPantheRAnnotation object being reset:") }
# targetFeatTable (cpdID, cpdName, ROI), uROI, FIR, cpdMetadata
resetTarg <- resetAnnot_targetFeatTable_uROI_FIR_cpdMeta(previousAnnotation,
targetFeatTable, uROI, FIR, cpdMetadata, verbose)
.targetFeatTable <- resetTarg$target
.uROI <- resetTarg$uROI
.FIR <- resetTarg$FIR
.cpdMetadata <- resetTarg$cpd
# spectraPaths, spectraMetadata
resSpectra <- resetAnnot_spectraPathMetadata(previousAnnotation,
spectraPaths, spectraMetadata, verbose)
.spectraPaths <- resSpectra$spectraPaths
.spectraMetadata <- resSpectra$spectraMetadata
# uROIExist
.uROIExist <- resetAnnot_uROIExist(uROIExist, targetFeatTable,
previousAnnotation, verbose)
# useUROI, useFIR
resUSE <- resetAnnot_useUROIuseFIR(useUROI, useFIR, targetFeatTable,
previousAnnotation, verbose)
.useUROI <- resUSE$useUROI
.useFIR <- resUSE$useFIR
# is annotated
.isAnnotated <- FALSE
# Create new object In all case (old or new value) spectraPaths and
# targetFeatTable will trigger the resetting of all results
peakPantheRAnnotation(spectraPaths = .spectraPaths,
targetFeatTable = .targetFeatTable, uROI = .uROI, FIR = .FIR,
cpdMetadata = .cpdMetadata, spectraMetadata = .spectraMetadata,
uROIExist = .uROIExist, useUROI = .useUROI, useFIR = .useFIR,
isAnnotated = .isAnnotated, ...)
})
# resetAnnotation targetFeatTable (cpdID, cpdName, ROI), uROI, FIR, cpdMetadata
resetAnnot_targetFeatTable_uROI_FIR_cpdMeta <- function(previousAnnotation,
targetFeatTable, uROI, FIR, cpdMetadata, verbose) {
# reuse previous values
if (all(is.null(targetFeatTable))) {
reset <- resetAnnot_prevTargetFeatTable(previousAnnotation, uROI, FIR,
cpdMetadata, verbose)
} else {
# reset to default
reset <- resetAnnot_newTargetFeatTable(targetFeatTable, uROI, FIR,
cpdMetadata, verbose)
}
return(reset)
}
# resetAnnotation reuse previous targetFeatTable
resetAnnot_prevTargetFeatTable <- function(previousAnnotation, uROI, FIR,
cpdMetadata, verbose) {
# previous values
.targetFeatTable <- ROI(previousAnnotation)
if (verbose) {
message(" Previous \"ROI\", \"cpdID\" and \"cpdName\" value kept")
}
# uROI
if (all(is.null(uROI))) { # previous values
.uROI <- uROI(previousAnnotation)[, c("rtMin", "rt", "rtMax",
"mzMin", "mz", "mzMax")]
if (verbose) {
message(" Previous \"uROI\" value kept")
}
} else { # new value
.uROI <- uROI
if (verbose) {
message(" New \"uROI\" value set")
}
}
# FIR
if (all(is.null(FIR))) { # previous values
.FIR <- FIR(previousAnnotation)[, c("rtMin", "rtMax", "mzMin",
"mzMax")]
if (verbose) {
message(" Previous \"FIR\" value kept")
}
} else { # new value
.FIR <- FIR
if (verbose) {
message(" New \"FIR\" value set")
}
}
# cpdMetadata
if (all(is.null(cpdMetadata))) { # previous values
.cpdMetadata <- cpdMetadata(previousAnnotation)
if (verbose) {
message(" Previous \"cpdMetadata\" value kept")
}
} else { # new value
.cpdMetadata <- cpdMetadata
if (verbose) {
message(" New \"cpdMetadata\" value set")
}
}
return(list(target=.targetFeatTable, uROI=.uROI, FIR=.FIR,
cpd=.cpdMetadata))
}
# resetAnnotation new targetFeatTable
resetAnnot_newTargetFeatTable <- function(targetFeatTable, uROI, FIR,
cpdMetadata, verbose) {
# reset to default
.targetFeatTable <- targetFeatTable
if (verbose) {
message(' New \"targetFeatTable\" value set (\"ROI\", ',
'\"cpdID\", \"cpdName\"') }
# uROI
if (all(is.null(uROI))) {
# Do not reuse old values if we change the compounds targeted
.uROI <- data.frame(rtMin = numeric(), rt = numeric(),
rtMax = numeric(), mzMin = numeric(), mz = numeric(),
mzMax = numeric(), stringsAsFactors = FALSE)
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"uROI\" cannot be kept and set to default') }
} else { # new value
.uROI <- uROI
if (verbose) { message(" New \"uROI\" value set") }
}
# FIR
if (all(is.null(FIR))) {
# Do not reuse old values if we change the compounds targeted
.FIR <- data.frame(rtMin = numeric(), rtMax = numeric(),
mzMin = numeric(), mzMax = numeric(), stringsAsFactors = FALSE)
if (verbose) {
message(' Targeted compounds changed, previous \"FIR\"',
' cannot be kept and set to default')
}
} else { # new value
.FIR <- FIR
if (verbose) { message(" New \"FIR\" value set") }
}
# cpdMetadata
if (all(is.null(cpdMetadata))) {
# Do not reuse old values if we change the compounds targeted
.cpdMetadata <- data.frame()
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"cpdMetadata\" cannot be kept and set to default')
}
} else { # new value
.cpdMetadata <- cpdMetadata
if (verbose) { message(" New \"cpdMetadata\" value set") }
}
return(list(target=.targetFeatTable, uROI=.uROI, FIR=.FIR,
cpd=.cpdMetadata))
}
# resetAnnotation spectraPaths, spectraMetadata
resetAnnot_spectraPathMetadata <- function(previousAnnotation, spectraPaths,
spectraMetadata, verbose) {
# reuse previous values
if (all(is.null(spectraPaths))) {
.spectraPaths <- filepath(previousAnnotation)
if (verbose) {
message(" Previous \"filepath\" value kept")
}
# spectraMetadata
if (all(is.null(spectraMetadata))) {
# previous values
.spectraMetadata <- spectraMetadata(previousAnnotation)
if (verbose) {
message(" Previous \"spectraMetadata\" value kept")
}
} else {
# new value
.spectraMetadata <- spectraMetadata
if (verbose) {
message(" New \"spectraMetadata\" value set")
}
}
# new values
} else {
.spectraPaths <- spectraPaths
if (verbose) {
message(" New \"spectraPaths\" value set")
}
# spectraMetadata
if (all(is.null(spectraMetadata))) {
# Do not reuse old values if we change the spectra
.spectraMetadata <- data.frame()
if (verbose) {
message(' Targeted spectra changed, previous ',
'\"spectraMetadata\" cannot be kept and set to default')
}
} else {
# new value
.spectraMetadata <- spectraMetadata
if (verbose) {
message(" New \"spectraMetadata\" value set")
}
}
}
return(list(spectraPaths = .spectraPaths,
spectraMetadata = .spectraMetadata))
}
# resetAnnotation uROIExist
resetAnnot_uROIExist <- function(uROIExist, targetFeatTable, previousAnnotation,
verbose) {
if (all(is.null(uROIExist))) {
# previous values cannot be used if targetFeatTable is changed
if (all(is.null(targetFeatTable))) {
# previous values
.uROIExist <- uROIExist(previousAnnotation)
if (verbose) {
message(" Previous \"uROIExist\" value kept")
}
} else {
# Do not reuse old values if we change the compounds
.uROIExist <- FALSE
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"uROIExist\" cannot be kept and set to default')
}
}
} else {
# new value
.uROIExist <- uROIExist
if (verbose) {
message(" New \"uROIExist\" value set")
}
}
return(.uROIExist)
}
# resetAnnotation useUROI, useFIR
resetAnnot_useUROIuseFIR <- function(useUROI, useFIR, targetFeatTable,
previousAnnotation, verbose){
# useUROI
if (all(is.null(useUROI))) {
# previous values cannot be used if targetFeatTable is changed
if (all(is.null(targetFeatTable))) {
# previous values
.useUROI <- useUROI(previousAnnotation)
if (verbose) {
message(" Previous \"useUROI\" value kept")
}
} else {
# Do not reuse old values if we change the compound
.useUROI <- FALSE
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"useUROI\" cannot be kept and set to default')
}
}
} else { # new value
.useUROI <- useUROI
if (verbose) { message(" New \"useUROI\" value set") }
}
# useFIR
if (all(is.null(useFIR))) {
# previous values cannot be used if targetFeatTable is changed
if (all(is.null(targetFeatTable))) {
# previous values
.useFIR <- useFIR(previousAnnotation)
if (verbose) {
message(" Previous \"useFIR\" value kept")
}
} else { # Do not reuse old values if we change the compound
.useFIR <- FALSE
if (verbose) {
message(' Targeted compounds changed, previous ',
'\"useFIR\" cannot be kept and set to default')
}
}
} else { # new value
.useFIR <- useFIR
if (verbose) { message(" New \"useFIR\" value set") }
}
return(list(useUROI = .useUROI, useFIR = .useFIR))
}
## Reset FIR windows to uROI or ROI values
setGeneric("resetFIR",
function(object, verbose = TRUE, ...)
standardGeneric("resetFIR"))
#' Reset FIR windows to uROI or ROI values
#' Reset FIR windows to uROI (or ROI if \code{uROIExist=FALSE})
#' @param object (peakPantheRAnnotation) object for which FIR are to be reset
#' @param verbose (bool) If TRUE message progress
#' @return (peakPantheRAnnotation) object with FIR values reset
#' @docType methods
#' @aliases resetFIR
#' @export
#' @examples
#' ## Initialise a peakPantheRAnnotation object with 2 targeted compounds
#'
#' ## targetFeatTable
#' input_targetFeatTable <- data.frame(matrix(vector(), 2, 8,
#' dimnames=list(c(), c('cpdID', 'cpdName', 'rtMin',
#' 'rt', 'rtMax', 'mzMin', 'mz', 'mzMax'))),
#' stringsAsFactors=FALSE)
#' input_targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3., 1., 4., 5., 2., 6.)
#' input_targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 19., 17., 20., 21., 18., 22.)
#' input_targetFeatTable[,c(3:8)] <- sapply(input_targetFeatTable[,c(3:8)],
#' as.numeric)
#' ## FIR
#' input_FIR <- data.frame(matrix(vector(), 2, 4, dimnames=list(c(),
#' c('rtMin', 'rtMax', 'mzMin', 'mzMax'))),
#' stringsAsFactors=FALSE)
#' input_FIR[1,] <- c(13., 14., 15., 16.)
#' input_FIR[2,] <- c(29., 30., 31., 32.)
#'
#' annotation <- peakPantheRAnnotation(targetFeatTable = input_targetFeatTable,
#' FIR = input_FIR, uROIExist = FALSE)
#'
#' ## Reset FIR with ROI values as uROI are not set
#' updatedAnnotation <- resetFIR(annotation, verbose=TRUE)
#' # FIR will be reset with ROI values as uROI values are not set
setMethod("resetFIR", "peakPantheRAnnotation",
function(object, verbose) {
# uROI exist
if (uROIExist(object)) {
if (verbose) {
message("FIR will be reset with uROI values")
}
newFIR <- uROI(object)[, c("rtMin", "rtMax", "mzMin", "mzMax")]
# uROI not defined
} else {
if (verbose) {
message('FIR will be reset with ROI values as uROI values ',
'are not set')
}
newFIR <- ROI(object)[, c("rtMin", "rtMax", "mzMin", "mzMax")]
}
object@FIR[, c("rtMin", "rtMax", "mzMin", "mzMax")] <-
newFIR[, c("rtMin", "rtMax", "mzMin", "mzMax")]
return(object)
})
#####################################################################
# Retention time correction: adjust uROI rt based on previously integrated
# signal
setGeneric("retentionTimeCorrection",
function(annotationObject, rtCorrectionReferences=NULL,
method='polynomial', params=list(polynomialOrder=2),
robust=FALSE, rtWindowWidth=15, diagnostic=TRUE)
standardGeneric("retentionTimeCorrection"))
#' @title Apply retention time correction methods to adjust the retention time
#' information in the uROI of peakPantheRAnnotation object
#' @description Performs retention time correction to re-adjust the expected
#' retention time position of compounds.
#' Requires an annotated peakPantheRAnnotation object (\code{isAnnotated=TRUE}).
#' The original \code{rt} value is used as expected and the observed deviation
#' measured in the \code{rt_dev_sec} field is taken as the deviation to be
#' corrected.
#' @param annotationObject (peakPantheRAnnotation) object with previous fit
#' results to adjust retention time values in uROI and FIR
#' annotationObject, rtCorrectionReferences=NULL,
#' @param rtCorrectionReferences (list) of compounds IDs (\code{cpdID})
#' to be used as retention time references.
#' All \code{cpdID} entries must be present in the object and previously
#' annotated. If NULL, use all compounds.
#' @param method (str) name of RT correction method to use (currently
#' \code{polynomial} or \code{constant}
#' @param params (list) list of parameters to pass to each correction method.
#' Currently allowed inputs are \code{polynomialOrder}
#' for \code{method='polynomial'}
#' @param robust (bool) whether to use the RANSAC algorithm to flag and ignore
#' outliers during retention time correction
#' @param rtWindowWidth (numeric) full width in seconds
#' of the retention time window defined around the corrected retention time
#' value for each compound
#' @param diagnostic (bool) If TRUE returns diagnostic plots (specific to each
#' correction method)
#' @return (list) containing entries `annotation`, with the new and retention
#' time corrected peakPantheRAnnotation, and `plot` (if \code{diagnostic=TRUE}).
#' @docType methods
#' @aliases retentionTimeCorrection
#' @export
#' @examples
#' if(requireNamespace('faahKO')){
#' ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
#' ## compounds
#'
#' # Paths to spectra files
#' library(faahKO)
#' spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
#' system.file('cdf/KO/ko16.CDF', package = 'faahKO'))
#'
#' # targetFeatTable
#' targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
#' c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
#' 'mzMax'))), stringsAsFactors=FALSE)
#' targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
#' 522.2, 522.205222)
#' targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
#' 496.2, 496.204962)
#' targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
#' FUN.VALUE=numeric(2))
#'
#' smallAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
#' targetFeatTable=targetFeatTable)
#' # annotate files serially
#' annotation_result <- peakPantheR_parallelAnnotation(smallAnnotation,
#' ncores=0, verbose=TRUE)
#' data_annotation <- annotation_result$annotation
#'
#' # Example with constant correction
#' rtCorrectionOutput <- retentionTimeCorrection(
#' annotationObject = data_annotation,
#' rtCorrectionReferences=c('ID-1'),
#' method='constant', params=list(),
#' robust=FALSE,
#' rtWindowWidth=15,
#' diagnostic=TRUE)
#'
#' rtCorrectedAnnotation <- rtCorrectionOutput$annotation
#'
#' # rtCorrectedAnnotation
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 2 samples.
#' # updated ROI exists, with a modified rt (uROI)
#' # uses updated ROI (uROI)
#' # uses fallback integration regions (FIR)
#' # is annotated
#'
#' rtCorrectionPlot <- rtCorrectionOutput$plot
#' # rtCorrectedPlot
#' # A ggplot2 object
#' # Scatterplot where x=`r` in the and y=`rt_dev_sec` from data_annotation
#' # Points colored depending on whether the reference was used to fit
#' # the correction model
#' }
setMethod("retentionTimeCorrection", "peakPantheRAnnotation",
function(annotationObject, rtCorrectionReferences, method, params, robust,
rtWindowWidth, diagnostic) {
newAnnotation <- annotationObject
rtCorrectionReferences <- rtCorrection_checkInput(newAnnotation,
rtCorrectionReferences,rtWindowWidth)
featureInformation <-
rtCorrection_prepareTargetFeatTable(newAnnotation,
rtCorrectionReferences)
referenceTable <- featureInformation$referenceTable
targetFeatTable <- featureInformation$targetFeatTable
newAnnotation <- rtCorrection_prepareAnnotation(newAnnotation,
targetFeatTable, rtWindowWidth)
referenceTable <- referenceTable[!is.na(referenceTable$rt_dev_sec), ]
correctedRtTable <-
peakPantheR_applyRTCorrection(
targetFeatTable[!is.na(targetFeatTable$rt_dev_sec), ],
referenceTable, method,
params, robust)
# Only compounds with measured rt_dev_sec can be adjusted
newAnnotation@uROI[!is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
correctedRtTable$correctedRt - (rtWindowWidth/2)
newAnnotation@uROI[!is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
correctedRtTable$correctedRt + (rtWindowWidth/2)
newAnnotation@uROI[!is.na(targetFeatTable$rt_dev_sec), "rt"] <-
correctedRtTable$correctedRt
newAnnotation@FIR[!is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
correctedRtTable$correctedRt - (rtWindowWidth/2)
newAnnotation@FIR[!is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
correctedRtTable$correctedRt + (rtWindowWidth/2)
if (isTRUE(diagnostic)) {
rtAdjustmentPlot <-
rtCorrection_diagnosticPlot(correctedRtTable)
return(list(annotation=newAnnotation, plot=rtAdjustmentPlot))
} else {return(list(annotation=newAnnotation))}
})
# Helper functions for the retentionTimeCorrection method
rtCorrection_checkInput <- function(annotation, rtCorrectionReferences,
rtWindowWidth) {
if (isFALSE(annotation@isAnnotated)) {
stop(paste('The retention time correction functionality requires an',
'annotated peakPantheRAnnotation object',
'(annotationObject@isAnnotated = TRUE)'))
}
if (is.null(rtCorrectionReferences)) {
rtCorrectionReferences <- annotation@cpdID
} else {
if (!all(rtCorrectionReferences %in% annotation@cpdID)) {
stop(paste('All compound IDs in rtCorrectionReferences must be',
'present on the annotationObject'))
}
}
if (isFALSE(is.numeric(rtWindowWidth)) | rtWindowWidth <= 0) {
stop('rtWindowWidth must be a positive number')
}
return(rtCorrectionReferences)
}
# Helper functions for the retentionTimeCorrection method
rtCorrection_prepareTargetFeatTable <- function(newAnnotation,
rtCorrectionReferences) {
# Obtain the mean retention time deviation per second
rt_dev_secMatrix <- annotationTable(newAnnotation,"rt_dev_sec")
rt_dev_sec_mean <- unname(vapply(rt_dev_secMatrix, mean, na.rm=TRUE,
FUN.VALUE = numeric(1)))
# If uROI exists and useROI was set to true, use that value as original RT,
# otherwise the "theoretical rt" is taken from ROI
if (newAnnotation@uROIExist & newAnnotation@useUROI) {
rt_expected <- newAnnotation@uROI[, "rt"]
} else { rt_expected <- newAnnotation@ROI[, "rt"] }
targetFeatTable <- data.frame(cpdID=newAnnotation@cpdID,
cpdName=newAnnotation@cpdName, rt=rt_expected,
rt_dev_sec=rt_dev_sec_mean)
# subset the references from the table of all compounds to correct
referenceTable <- targetFeatTable[targetFeatTable$cpdID
%in% rtCorrectionReferences, ]
# Exclude features with mean rt_dev_sec = NA from the correction
# function fitting
if (any(is.na(referenceTable$rt_dev_sec))) {
warning(paste("The following references could not be integrated",
"previously and will be excluded:",
referenceTable[is.na(referenceTable$rt_dev_sec), "cpdID"]))
}
if (any(is.na(targetFeatTable$rt_dev_sec))) {
warning(paste("The following compounds could not be",
"integrated previously and will be not be corrected:",
targetFeatTable[is.na(targetFeatTable$rt_dev_sec), "cpdID"]))
}
return(list(targetFeatTable=targetFeatTable,
referenceTable=referenceTable))
}
# Helper functions for the retentionTimeCorrection method
rtCorrection_prepareAnnotation <-function(newAnnotation, targetFeatTable,
rtWindowWidth) {
if (isFALSE(newAnnotation@useUROI)) {
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] <-
newAnnotation@ROI[is.na(targetFeatTable$rt_dev_sec), "rt"]
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] -
(rtWindowWidth/2)
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] +
(rtWindowWidth/2)
newAnnotation@FIR[is.na(targetFeatTable$rt_dev_sec), "rtMin"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] -
(rtWindowWidth/2)
newAnnotation@FIR[is.na(targetFeatTable$rt_dev_sec), "rtMax"] <-
newAnnotation@uROI[is.na(targetFeatTable$rt_dev_sec), "rt"] +
(rtWindowWidth/2)
}
# set uROIExist to TRUE
# after corrrection useUROI is TRUE as corrected info is updated there
newAnnotation@uROIExist <- TRUE
newAnnotation@useUROI <- TRUE
return(newAnnotation)
}
rtCorrection_diagnosticPlot <- function(correctedRtTable) {
rtAdjustmentPlot <- ggplot2::ggplot(data=correctedRtTable) +
ggplot2::geom_point(ggplot2::aes(x=rt,
y=rt_dev_sec, col=isReference)) +
ggplot2::geom_line(ggplot2::aes(x=rt,
y=predictedRtDrift))
rtAdjustmentPlot <- rtAdjustmentPlot +
ggplot2::xlab('Retention time') +
ggplot2::ylab('Retention time deviation')
return(rtAdjustmentPlot)
}
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