nbinomTestForMatrices {DESeq} | R Documentation

## Perform row-wise tests for differences between the base means of two count matrices.

### Description

This function is called by `nbinomTest`. Call it directly only if the S4 interface is unsuitable for your task.

### Usage

    nbinomTestForMatrices(countsA, countsB, sizeFactorsA, sizeFactorsB, dispsA, dispsB )

### Arguments

`countsA` | A matrix of counts, where each column is a replicate
`countsB` | Another matrix of counts, where each column is a replicate
`sizeFactorsA` | Size factors for the columns of the matrix 'countsA'
`sizeFactorsB` | Size factors for the columns of the matrix 'countsB'
`dispsA` | The dispersions for 'countsA', a vector with one value per gene
`dispsB` | The same for 'countsB'

### Details

See the vignette for an exact description of the null hypothesis tested.

### Value

A vector of unadjusted p values, one for each row in the counts matrices.

### Author(s)

Simon Anders, sanders@fs.tum.de

### Examples

    cds <- makeExampleCountDataSet()
    cds <- estimateSizeFactors( cds )
    cds <- estimateDispersions( cds, method="per-condition" )
    colsA <- conditions(cds) == "A"
    colsB <- conditions(cds) == "B"
    bmvA <- getBaseMeansAndVariances( counts(cds)[,colsA], sizeFactors(cds)[colsA] )
    bmvB <- getBaseMeansAndVariances( counts(cds)[,colsB], sizeFactors(cds)[colsB] )
    pvals <- nbinomTestForMatrices(
       counts(cds)[,colsA],
       counts(cds)[,colsB],
       sizeFactors(cds)[colsA],
       sizeFactors(cds)[colsB],
       fitInfo(cds,"A")$dispFunc( rowMeans( counts( cds, normalized=TRUE ) ) ),
       fitInfo(cds,"B")$dispFunc( rowMeans( counts( cds, normalized=TRUE ) ) ) )
    names( pvals ) <- row.names( counts(cds) )
    head( pvals )

    # This here should give the same results:
    head( nbinomTest( cds, "A", "B" )$pval )

[Package DESeq version 1.36.0 Index]