normalizeDeseq2 {metaseqR2} | R Documentation

## Normalization based on the DESeq2 package

### Description

This function is a wrapper over DESeq2 normalization. It accepts a matrix of gene counts (e.g. produced by importing an externally generated table of counts to the main metaseqr2 pipeline).

### Usage

        normalizeDeseq2(geneCounts, sampleList,
            normArgs = NULL, output = c("matrix", "native"))

### Arguments

`geneCounts` | a table where each row represents a gene and each column a sample. Each cell contains the read counts for each gene and sample. Such a table can be produced outside metaseqr2 and is imported during the basic metaseqr2 workflow.
`sampleList` | the list containing condition names and the samples under each condition.
`normArgs` | a list of DESeq normalization parameters. See the result of `getDefaults("normalization",` `"deseq")` for an example and how you can modify it.
`output` | the class of the output object. It can be `"matrix"` (default) for versatility with other tools or `"native"` for the DESeq2 native S4 object (DESeqDataSet). In the latter case it should be handled with suitable DESeq2 methods.

### Value

A matrix or a DESeqDataSet with normalized counts.

### Author(s)

Dionysios Fanidis

### Examples

    dataMatrix <- metaseqR2:::exampleCountData(2000)
    sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
    diagplotBoxplot(dataMatrix,sampleList)

    normDataMatrix <- normalizeDeseq2(dataMatrix,sampleList)
    diagplotBoxplot(normDataMatrix,sampleList)

[Package metaseqR2 version 1.2.0 Index]