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$count) countData$count<-apply(countData$count,2,function(x) as.numeric(x)) g_keep <- apply(countData$count,1,function(x) sum(x>0)>5) countData$count<-countData$count[g_keep,] countTableTMM<-ROSeq::TMMnormalization(countData$count) countTableTMM