inst/doc/getting-started.R

In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

## ----biocstyle, echo = FALSE, results = "asis"--------------------------------
BiocStyle::markdown()

## ---- echo = FALSE------------------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

## ----init, message = FALSE, echo = FALSE, results = "hide"--------------------
## Silently loading all packages
library(BiocStyle)
library(peakPantheR)
library(faahKO)
library(pander)

## ---- eval = FALSE------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("peakPantheR")

## ---- eval = FALSE------------------------------------------------------------
#  # Install devtools
#  if(!require("devtools")) install.packages("devtools")
#  devtools::install_github("phenomecentre/peakPantheR")

## ---- eval = FALSE------------------------------------------------------------
#  library(peakPantheR)
#  
#  peakPantheR_start_GUI(browser = TRUE)
#  #  To exit press ESC in the command line

## ---- fig.align="center", out.width = "700px", echo = FALSE-------------------
knitr::include_graphics("../man/figures/example-UI.png")

## ---- eval = FALSE------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("faahKO")

## -----------------------------------------------------------------------------
library(faahKO)
## file paths
input_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"))
input_spectraPaths

## ---- eval=FALSE--------------------------------------------------------------
#  # 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(1, "Cpd 1", 3310., 3344.888, 3390., 522.194778,
#                                  522.2, 522.205222)
#  input_targetFeatTable[2,] <- c(2, "Cpd 2", 3280., 3385.577, 3440., 496.195038,
#                                  496.2, 496.204962)
#  input_targetFeatTable[,c(1,3:8)] <- sapply(input_targetFeatTable[,c(1,3:8)],
#                                              as.numeric)

## ---- results = "asis", echo = FALSE------------------------------------------
# use pandoc for improved readability
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(1, "Cpd 1", 3310., 3344.888, 3390., 522.194778, 
                                522.2, 522.205222)
input_targetFeatTable[2,] <- c(2, "Cpd 2", 3280., 3385.577, 3440., 496.195038,
                                496.2, 496.204962)
input_targetFeatTable[,c(1,3:8)] <- sapply(input_targetFeatTable[,c(1,3:8)], 
                                            as.numeric)
rownames(input_targetFeatTable) <- NULL
pander::pandoc.table(input_targetFeatTable, digits = 9)

## ---- eval=FALSE--------------------------------------------------------------
#  library(faahKO)
#  
#  # Define the file paths (3 samples)
#  input_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"))
#  
#  # Define the targeted features (2 features)
#  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", 3310., 3344.888, 3390.,
#                                  522.194778, 522.2, 522.205222)
#  input_targetFeatTable[2,] <- c("ID-1", "Cpd 2", 3280., 3385.577, 3440.,
#                                  496.195038, 496.2, 496.204962)
#  input_targetFeatTable[,3:8] <- sapply(input_targetFeatTable[,3:8], as.numeric)
#  
#  # Define some random compound and spectra metadata
#  # cpdMetadata
#  input_cpdMetadata     <- data.frame(matrix(data=c('a','b',1,2), nrow=2, ncol=2,
#                              dimnames=list(c(), c('testcol1','testcol2')),
#                              byrow=FALSE), stringsAsFactors=FALSE)
#  # spectraMetadata
#  input_spectraMetadata <- data.frame(matrix(data=c('c','d','e',3,4,5), nrow=3,
#                              ncol=2,
#                              dimnames=list(c(),c('testcol1','testcol2')),
#                              byrow=FALSE), stringsAsFactors=FALSE)
#  
#  # Initialise a simple peakPantheRAnnotation object
#  # [3 files, 2 features, no uROI, no FIR]
#  initAnnotation <- peakPantheRAnnotation(spectraPaths=input_spectraPaths,
#                                          targetFeatTable=input_targetFeatTable,
#                                          cpdMetadata=input_cpdMetadata,
#                                          spectraMetadata=input_spectraMetadata)
#  
#  # Rename and save the annotation to disk
#  annotationObject <- initAnnotation
#  save(annotationObject,
#          file = './example_annotation_ppR_UI.RData',
#          compress=TRUE)
#  

## ---- eval=FALSE--------------------------------------------------------------
#  # Define targeted features without uROI and FIR (2 features)
#  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", 3310., 3344.888, 3390.,
#                                  522.194778, 522.2, 522.205222)
#  input_targetFeatTable[2,] <- c("ID-1", "Cpd 2", 3280., 3385.577, 3440.,
#                                  496.195038, 496.2, 496.204962)
#  input_targetFeatTable[,3:8] <- sapply(input_targetFeatTable[,3:8], as.numeric)
#  
#  # save to disk
#  write.csv(input_targetFeatTable,
#              file = './1-fitParams_example_UI.csv',
#              row.names = FALSE)

## ---- results = "asis", echo = FALSE------------------------------------------
# use pandoc for improved readability
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", 3310., 3344.888, 3390.,
                                522.194778, 522.2, 522.205222)
input_targetFeatTable[2,] <- c("ID-1", "Cpd 2", 3280., 3385.577, 3440.,
                                496.195038, 496.2, 496.204962)
input_targetFeatTable[,3:8] <- sapply(input_targetFeatTable[,3:8], as.numeric)
rownames(input_targetFeatTable) <- NULL
pander::pandoc.table(input_targetFeatTable, digits = 9)

## ---- eval=FALSE--------------------------------------------------------------
#  # Define the spectra paths and metada
#  input_spectraMeta <- data.frame(matrix(vector(), 3, 3,
#                          dimnames=list(c(),c("filepath","testcol1","testcol2"))),
#                          stringsAsFactors=FALSE)
#  input_spectraMeta[1,] <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
#                              "c", 3)
#  input_spectraMeta[2,] <- c(system.file('cdf/KO/ko16.CDF', package = "faahKO"),
#                              "d", 4)
#  input_spectraMeta[3,] <- c(system.file('cdf/KO/ko18.CDF', package = "faahKO"),
#                              "e", 5)
#  
#  # save to disk
#  write.csv(input_spectraMeta,
#              file = './2-spectraMetaWPath_example_UI.csv',
#              row.names = FALSE)

## ---- results = "asis", echo = FALSE------------------------------------------
# use pandoc for improved readability
input_spectraMeta <- data.frame(matrix(vector(), 3, 3,
                        dimnames=list(c(),c("filepath","testcol1","testcol2"))),
                        stringsAsFactors=FALSE)
input_spectraMeta[1,] <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
                            "c", 3)
input_spectraMeta[2,] <- c(system.file('cdf/KO/ko16.CDF', package = "faahKO"),
                            "d", 4)
input_spectraMeta[3,] <- c(system.file('cdf/KO/ko18.CDF', package = "faahKO"),
                            "e", 5)
rownames(input_spectraMeta) <- NULL
pander::pandoc.table(input_spectraMeta, digits = 0)

## ---- eval=FALSE--------------------------------------------------------------
#  # Define the feature metada
#  input_featMeta <- data.frame(matrix(vector(), 2, 2,
#                      dimnames=list(c(),c("testcol1","testcol2"))),
#                      stringsAsFactors=FALSE)
#  input_featMeta[1,] <- c("a", 1)
#  input_featMeta[2,] <- c("b", 2)
#  
#  # save to disk
#  write.csv(input_featMeta,
#              file = './3-featMeta_example_UI.csv',
#              row.names = FALSE)

## ---- results = "asis", echo = FALSE------------------------------------------
# use pandoc for improved readability
input_featMeta <- data.frame(matrix(vector(), 2, 2,
                    dimnames=list(c(),c("testcol1","testcol2"))),
                    stringsAsFactors=FALSE)
input_featMeta[1,] <- c("a", 1)
input_featMeta[2,] <- c("b", 2)
rownames(input_featMeta) <- NULL
pander::pandoc.table(input_featMeta, digits = 0)