nbinomTest: Test for differences between the base means for two...

In DESeq: Differential gene expression analysis based on the negative binomial distribution

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, [e-mail]

Examples

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

DESeq documentation built on April 28, 2020, 6:37 p.m.