R/soma2eset.R

In graumannlab/readat: Functionality to Read and Manipulate SomaLogic ADAT files

# Project: readat
#
# Author: Aditya Bhagwat
###############################################################################


#' Convert objects into ExpressionSets or MSnSets.
#'
#' Converts objects into \code{ExpressionSet} or \code{MSnSet} instances.
#' @param x An object to transform.  Currently only \code{WideSomaLogicData}
#' objects are supported.
#' @param somaObj A \code{WideSomaLogicData} object to transform.
#' @param log2Transform whether to log2 transform intensities or not
#' @param ... Passed between methods.
#' @return ExpressionSet or MSnSet object
#' @author Aditya Bhagwat
#' @examples
#' somaFile <- extractSampleData()
#' wideSomaData <- readAdat(somaFile)
#' as.ExpressionSet(wideSomaData)
#' if(requireNamespace("MSnbase"))
#' {
#'     as.MSnSet(wideSomaData)
#' }
#'
#' unlink(somaFile)
#' @importFrom Biobase annotation<-
#' @importFrom Biobase ExpressionSet
#' @importFrom Biobase exprs exprs<-
#' @importFrom Biobase pData
#' @importFrom Biobase fData
#' @export
as.ExpressionSet <- function(x, log2Transform = TRUE, ...)
{
    UseMethod("as.ExpressionSet")
}

#' @rdname as.ExpressionSet
#' @export
as.ExpressionSet.WideSomaLogicData <- function(x, log2Transform = TRUE, ...)
{
    soma2eset(x, log2Transform = log2Transform)
}

#' @rdname as.ExpressionSet
#' @importFrom Biobase   annotation<-   experimentData<-   preproc<-
#' @export
soma2eset <- function(somaObj, log2Transform = TRUE){

    # assayData
    myIntensities <- getIntensities(
        somaObj, rowsContain = "sequences", reorder = TRUE
    )
    myMeta <- getMetadata(somaObj)

    # fData
    featureDF <- getSequenceData(somaObj)
    featureDF <- data.frame(featureDF, row.names = featureDF$SeqId)

    # pData
    sampleDF <- getSampleData(somaObj)
    sampleDF <- data.frame(sampleDF, row.names = somaObj$ExtIdentifier)

    # forge eset
    myEset <- ExpressionSet(myIntensities)
    Biobase::pData(myEset) <- sampleDF
    Biobase::fData(myEset) <- featureDF
    Biobase::annotation(myEset) <- 'somascan'

    # log2 transform
    if (log2Transform){
        Biobase::exprs(myEset) <- log2(Biobase::exprs(myEset))
    }

    # Add preprocessing and annotation info
    parameters <- attributes(somaObj)$Metadata
    Biobase::preproc(Biobase::experimentData(myEset)) <-
        list(
            assay    = 'somascan',
            entity   = 'epitope',
            quantity = 'abundance',
            software = 'somalogic',
            parameters = parameters
        )
    Biobase::annotation(myEset) <- parameters$StudyOrganism

    # return eset
    return(myEset)
}

#' Is object a soma eset?
#' @param esetObj eSet
#' @return logical
#' @importFrom Biobase   experimentData   preproc
#' @export
isSomaEset <- function(esetObj){
    Biobase::preproc(Biobase::experimentData(esetObj))$assay == 'somascan'
}

#' Get name of sample id variable
#' @param somaEset eset with soma data
#' @return character
#' @examples
#' getSampleIdVar()
#' @export
getSampleIdVar <- function(somaEset){
    'SampleId'
}

#' @rdname as.ExpressionSet
#' @examples
#' if (interactive()) {
#'     # Not testing, since this is a repeat of readAdat() examples
#'     somaFile <- extractSampleData()
#'     wideSomaData <- readAdat(somaFile)
#'     as.ExpressionSet(wideSomaData)
#'     unlink(somaFile)
#' }
#' @export
as.MSnSet.WideSomaLogicData <- function(x, log2Transform = FALSE, ...)
{
    if(!requireNamespace("MSnbase", quietly = TRUE))
    {
        stop(
            'MSnbase is not available; try running\n',
            'BiocManager::install("MSnbase")'
        )
    }
    e <- as.ExpressionSet(x, log2Transform = log2Transform)
    MSnbase::as.MSnSet.ExpressionSet(e)
}

#' @rdname as.ExpressionSet
#' @export
as.MSnSet <- function(x, log2Transform = FALSE, ...)
{
    UseMethod("as.MSnSet")
}