DSpermute4GSEA {SeqGSEA} | R Documentation

## Compute NB-statistics quantifying differential splicing on the permutation data set.

### Description

This function is to calculate NB-statistics quantifying differential splicing for each gene on each permutation data set. The results will be used for GSEA run as DS background.

### Usage

    DSpermute4GSEA(RCS, permuteMat)

### Arguments

`RCS` | a ReadCountSet object after running `exonTestability`.
`permuteMat` | a permutation matrix generated by `genpermuteMat`.

### Details

Parallel running configuration: TODO

### Value

A ReadCountSet object with slot permute_NBstat_gene updated.

### Note

Please run `exonTestability` before run this function.

### 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

`exonTestability`, `genpermuteMat`, `DENBStatPermut4GSEA`, `DSpermutePval`

### Examples

    data(RCS_example, package="SeqGSEA")
    permuteMat <- genpermuteMat(RCS_example, times=10)
    RCS_example <- exonTestability(RCS_example)
    RCS_example <- DSpermute4GSEA(RCS_example, permuteMat)
    head(RCS_example@permute_NBstat_gene)

[Package SeqGSEA version 1.24.0 Index]