SeqGSEA (version 1.12.0)

DENBTest: Perform negative binomial exact test for differential expression

Description

Perform negative binomial exact test for differential expression - a modified version of nbinomTest in DESeq package.

Usage

DENBTest(cds)

Arguments

cds

A CountDataSet object with size factors and dispersion parameters estimated. Recommended to take the output of runDESeq.

Value

A data frame of the test results. Information contains mean expression values, NB-statistics, (log) fold-changes, p-values, and adjusted p-values.

References

Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data, Genome Biol, 11, R106.

See Also

runDESeq, DENBStat4GSEA

Examples

data(RCS_example, package="SeqGSEA")
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
DEGres <- DENBTest(DEG)
head(DEGres)