Commit 38225134 authored by Holger Brandl's avatar Holger Brandl

removed deprecated retainExprGenes and getExpressedGenes

parent 678f20d5
#require(cummeRbund)
filterByExpression <- function(fpkmMat, min_value=1){
stopifnot(is.numeric(min_value))
getExpressedGenes <- function(cuff, ...){
warning("DEPRECATED use filterByExpression instead")
fpkmMat<-cummeRbund::repFpkmMatrix(genes(cuff))
rownames(filterByExpression(fpkmMat, ...))
}
filterByExpression <- function(fpkmMat, minFPKM=1, logMode=F){
stopifnot(is.numeric(minFPKM))
if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount
# if(logMode) fpkmMat<-log10(fpkmMat+1) ## add a pseudocount
geneMax <- apply(fpkmMat, 1, max)
fpkmMat[geneMax>minFPKM,]
fpkmMat[geneMax>min_value,]
}
retainExprGenes <- function(df, id_col="ensembl_gene_id", ...){
warning("DEPRECATED Use filter_expressed_genes instead")
filter_expressed_genes(df, id_col, ...)
}
filter_expressed_genes <- function(df, id_col="ensembl_gene_id", ...){
......
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