SeqGSEA (version 1.12.0)

DSpermutePval: 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.

Value

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

Details

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

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))