nbinomTest {DESeq} | R Documentation

## Test for differences between the base means for two conditions

### Description

This function tests for differences between the base means of two conditions (i.e., for differential expression in the case of RNA-Seq).

### Usage

    nbinomTest(cds, condA, condB, pvals_only = FALSE, eps=NULL )

### Arguments

`cds` | a CountDataSet with size factors and raw variance functions
`condA` | one of the conditions in 'cds'
`condB` | another one of the conditions in 'cds'
`pvals_only` | return only a vector of (unadjusted) p values instead of the data frame described below.
`eps` | This argument is no longer used. Do not use it.

### Details

See `nbinomTestForMatrices` for more technical informations

### Value

A data frame with the following columns:

`id` | The ID of the observable, taken from the row names of the counts slots.
`baseMean` | The base mean (i.e., mean of the counts divided by the size factors) for the counts for both conditions
`baseMeanA` | The base mean (i.e., mean of the counts divided by the size factors) for the counts for condition A
`baseMeanB` | The base mean for condition B
`foldChange` | The ratio meanB/meanA
`log2FoldChange` | The log2 of the fold change
`pval` | The p value for rejecting the null hypothesis 'meanA==meanB'
`padj` | The adjusted p values (adjusted with 'p.adjust( pval, method="BH")')

### Author(s)

Simon Anders, sanders@fs.tum.de

### Examples

    cds <- makeExampleCountDataSet()
    cds <- estimateSizeFactors( cds )
    cds <- estimateDispersions( cds )
    head( nbinomTest( cds, "A", "B" ) )

[Package DESeq version 1.38.0 Index]