cummerutils.R

require.auto(cummeRbund)


getExpressedGenes <- function(cuff, minFPKM=1, logMode=F){
    fpkmMat<-repFpkmMatrix(genes(cuff))

    if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount

    geneMax <- apply(fpkmMat, 1, max)

    fpkmMat[geneMax>minFPKM,]$gene_id
}