From 38225134615909fb82bba4ad3bc9ad7b2247671c Mon Sep 17 00:00:00 2001 From: Holger Brandl Date: Thu, 31 Aug 2017 11:24:24 +0200 Subject: [PATCH] removed deprecated retainExprGenes and getExpressedGenes --- R/bio/diffex_commons.R | 24 ++++-------------------- 1 file changed, 4 insertions(+), 20 deletions(-) diff --git a/R/bio/diffex_commons.R b/R/bio/diffex_commons.R index 18268fb..fbbb731 100644 --- a/R/bio/diffex_commons.R +++ b/R/bio/diffex_commons.R @@ -1,31 +1,15 @@ -#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", ...){ -- GitLab