runDESeq {SeqGSEA} | R Documentation

## Run DESeq for differential expression analysis

### Description

This function provides a wrapper to run DESeq for differential expression analysis. It includes two steps, `DESeq::estimateSizeFactors` and `DESeq::estimateDispersions`.

### Usage

    runDESeq(geneCounts, label)

### Arguments

`geneCounts` | a matrix containing read counts for each gene, can be the output of `getGeneCount`.
`label` | the sample classification labels.

### Value

A CountDataSet object with size factors and dispersion parameters been estimated.

### 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

`getGeneCount`, `DENBTest`, `DENBStat4GSEA`

### Examples

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

[Package SeqGSEA version 1.30.0 Index]