DENBStatPermut4GSEA {SeqGSEA} | R Documentation

## Calculate NB-statistics quantifying DE for each gene in the permutation data sets

### Description

Calculate NB-statistics quantifying differential expression for each gene in the permutation data sets. The results will be used for GSEA run.

### Usage

    DENBStatPermut4GSEA(DEG, permuteMat)

### Arguments

`DEG` | a CountDataSet object, can be the output of `runDESeq`.
`permuteMat` | a permutation matrix generated by `genpermuteMat`.

### Value

A matrix of NB-statistics. Each row corresponds to each gene, and each column to each permutation.

### Note

The results with the output of `DENBStat4GSEA` 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

`DENBStat4GSEA`, `runDESeq`, `DEpermutePval`, `genpermuteMat`

### Examples

    data(RCS_example, package="SeqGSEA")
    permuteMat <- genpermuteMat(RCS_example, times=10)
    geneCounts <- getGeneCount(RCS_example)
    label <- label(RCS_example)
    DEG <- runDESeq(geneCounts, label)
    DEpermNBstat <- DENBStatPermut4GSEA(DEG, permuteMat)
    DEpermNBstat[1:10,1:10]

[Package SeqGSEA version 1.26.0 Index]