R/quantileNormalize.R

Defines functions quantileNorm

#library(preprocessCore)

#' @export
quantileNorm = function(whichFile,outFile=NULL){
    if (is.character(whichFile)){
        allDataPre = ogbox::read.exp(whichFile)
    } else{
        allDataPre = whichFile
    }
    
    list[geneData,exprData]= sepExpr(allDataPre)
    
    newExprData = preprocessCore::normalize.quantiles(as.matrix(exprData))
    # boxplot(newExprData)
    newExprData = as.data.frame(newExprData)
    colnames(newExprData) = colnames(exprData)
    newAllData = cbind(geneData, newExprData)
    if(is.character(outFile)){
        write.csv(newAllData, file = outFile, row.names=FALSE)
    }
    invisible(newAllData)
}
PavlidisLab/neuroExpressoAnalysis documentation built on Aug. 23, 2022, 7:42 a.m.