TMMnormalization {ROSeq} | R Documentation |
Trimmed Means of M values (TMM) normalization (on the basis of edgeR package)
TMMnormalization(countTable)
countTable |
The filtered, read count matrix, with row names as genes name/ID and column names as sample id/name |
countTableTMM
countData<-list() countData$count<-ROSeq::L_Tung_single$NA19098_NA19101_count countData$group<-ROSeq::L_Tung_single$NA19098_NA19101_group head(countData$count) gene_names<-rownames(countData$count) countData$count<-apply(countData$count,2,function(x) as.numeric(x)) rownames(countData$count)<-gene_names countData$count<-countData$count[,colSums(countData$count> 0) > 2000] g_keep <- apply(countData$count,1,function(x) sum(x>2)>=3) countData$count<-countData$count[g_keep,] countTableTMM<-ROSeq::TMMnormalization(countData$count) countTableTMM