DENBStat4GSEA {SeqGSEA} | R Documentation

## Calculate NB-statistics quantifying differential expression for each gene

### Description

Calculate NB-statistics quantifying differential expression between two groups of samples compared. The results will be used for GSEA run. Comparing with `DENBTest`, this function will not calculate NB test p-values.

This function only works with two-group comparison.

### Usage

    DENBStat4GSEA(cds)

### Arguments

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

### Value

A data frame containing each gene's expression means and variances in each group, and each gene's DE NB-statistics.

### Note

The results with the output of `DENBStatPermut4GSEA` can also be used to run `DEpermutePval`.

### Author(s)

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

### References

Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.

### See Also

`DENBTest`, `runDESeq`, `DENBStatPermut4GSEA`

### Examples

    data(RCS_example, package="SeqGSEA")
    geneCounts <- getGeneCount(RCS_example)
    label <- label(RCS_example)
    DEG <- runDESeq(geneCounts, label)
    DEGres <- DENBStat4GSEA(DEG)
    head(DEGres)

[Package SeqGSEA version 1.20.0 Index]