TMMnormalization {ROSeq} | R Documentation

## TMM Normalization.

### Description

Trimmed Means of M values (TMM) normalization (on the basis of edgeR package)

### Usage

    TMMnormalization(countTable)

### Arguments

`countTable` | The filtered, read count matrix, with row names as genes name/ID and column names as sample id/name

### Value

countTableTMM

### Examples

    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

[Package ROSeq version 1.2.10 Index]