SeqGSEA (version 1.12.0)

DSpermute4GSEA: 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.

Value

A ReadCountSet object with slot permute_NBstat_gene updated.

Details

Parallel running configuration: TODO

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)