Commit f4cf635e authored by Holger Brandl's avatar Holger Brandl

cont. cummerbund methods

parent 8332f533
require.auto(cummeRbund)
require(cummeRbund)
getExpressedGenes <- function(cuff, minFPKM=1, logMode=F){
getExpressedGenes <- function(cuff, ...){
fpkmMat<-repFpkmMatrix(genes(cuff))
rownames(filterByExpression(fpkmMat, ...))
}
filterByExpression <- function(fpkmMat, minFPKM=1, logMode=F){
if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount
geneMax <- apply(fpkmMat, 1, max)
rownames(fpkmMat[geneMax>minFPKM,])
fpkmMat[geneMax>minFPKM,]
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment