Commit 4aadc438 authored by Holger Brandl's avatar Holger Brandl

fixed expression filter

parent 93eff3c1
require.auto(cummeRbund) require.auto(cummeRbund)
getExpressedGenes <- function(cuff, minFPKM=1, logMode=F){ getExpressedGenes <- function(cuff, minFPKM=1, logMode=F){
fpkmMat<-repFpkmMatrix(genes(cuff)) fpkmMat<-repFpkmMatrix(genes(mmusCuff))
if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount
geneMax <- apply(fpkmMat, 1, max) geneMax <- apply(fpkmMat, 1, max)
fpkmMat[geneMax>minFPKM,]$gene_id rownames(fpkmMat[geneMax>minFPKM,])
} }
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