DSpermutePval {SeqGSEA} | R Documentation

## Permutation for p-values in differential splicing analysis

### Description

Calculate permutation p-values in differential splicing analysis.

### Usage

    DSpermutePval(RCS, permuteMat)

### Arguments

`RCS` | a ReadCountSet object after running `estiExonNBstat` and `estiGeneNBstat`.
`permuteMat` | a permutation matrix generated by `genpermuteMat`.

### Details

Permutation p-values are computed based on NB-statistics for comparison of the studied groups and NB-statistics from the permutation data sets.

### Value

A ReadCountSet object with slots `permute_NBstat_exon`, `permute_NBstat_gene`, `featureData`, and `featureData_gene` updated.

### 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

`estiExonNBstat`, `estiGeneNBstat`, `genpermuteMat`, `DSpermute4GSEA`

### Examples

    data(RCS_example, package="SeqGSEA")
    permuteMat <- genpermuteMat(RCS_example, times=10)
    RCS_example <- exonTestability(RCS_example)
    RCS_example <- estiExonNBstat(RCS_example)
    RCS_example <- estiGeneNBstat(RCS_example)
    RCS_example <- DSpermutePval(RCS_example, permuteMat)
    head(DSresultExonTable(RCS_example))
    head(DSresultGeneTable(RCS_example))

[Package SeqGSEA version 1.30.0 Index]