DSpermute4GSEA: Compute NB-statistics quantifying differential splicing on...
In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description Usage Arguments Details Value Note Author(s) References See Also Examples

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.

1	DSpermute4GSEA(RCS, permuteMat)

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

Parallel running configuration: TODO

A ReadCountSet object with slot permute_NBstat_gene updated.

Please run exonTestability before run this function.

Xi Wang, xi.wang@newcastle.edu.au

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.

exonTestability, genpermuteMat, DENBStatPermut4GSEA, DSpermutePval

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)