statDeseq2 {metaseqR2} | R Documentation

## Statistical testing with DESeq2

### Description

This function is a wrapper over DESeq statistical testing. It accepts a matrix of normalized gene counts or an S4 object specific to each normalization algorithm supported by metaseqR2.

### Usage

        statDeseq2(object, sampleList, contrastList = NULL,
            statArgs = NULL)

### Arguments

`object` | a matrix or an object specific to each normalization algorithm supported by metaseqR2, containing normalized counts. See also Details.
`sampleList` | the list containing condition names and the samples under each condition.
`contrastList` | vector of contrasts as defined in the main help page of `metaseqr2`. See also Details.
`statArgs` | a list of DESeq statistical algorithm parameters. See the result of `getDefaults("statistics",` `"deseq")` for an example and how you can modify it. It is not required when the input object is already a CountDataSet from DESeq normalization as the dispersions are already estimated.

### Details

Regarding `object`, apart from `matrix` (also for NOISeq), the object can be a `SeqExpressionSet` (EDASeq), `CountDataSet` (DESeq), `DGEList` (edgeR), `DESeqDataSet` (DESeq2), `SeqCountSet` (DSS) or `ABSDataSet` (ABSSeq).

Regarding `contrastList` it can also be a named structured list of contrasts as returned by the internal function `metaseqR2:::makeContrastList`.

### Value

A named list of p-values, whose names are the names of the contrasts.

### Author(s)

Dionysios Fanidis

### Examples

    require(DESeq2)
    dataMatrix <- metaseqR2:::exampleCountData(1000)
    sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
    contrast <- "A_vs_B"
    normDataMatrix <- normalizeDeseq2(dataMatrix,sampleList)
    p <- statDeseq2(normDataMatrix,sampleList,contrast)

[Package metaseqR2 version 1.0.11 Index]