R: Permutation for p-values in differential splicing analysis

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.

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 1.27.0 Index]