normalizeDeseq2: Normalization based on the DESeq2 package

Description Usage Arguments Value Author(s) Examples

View source: R/norm.R

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

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    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

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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)

metaseqR2 documentation built on Nov. 8, 2020, 7:34 p.m.