DENBTest {SeqGSEA} | R Documentation

## 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.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### 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)

[Package SeqGSEA version 1.30.0 Index]