DENBStatPermut4GSEA: Calculate NB-statistics quantifying DE for each gene in the...
In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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

Calculate NB-statistics quantifying differential expression for each gene in the permutation data sets. The results will be used for GSEA run.

1	DENBStatPermut4GSEA(DEG, permuteMat)

`DEG`	a CountDataSet object, can be the output of `runDESeq`.
`permuteMat`	a permutation matrix generated by `genpermuteMat`.

A matrix of NB-statistics. Each row corresponds to each gene, and each column to each permutation.

The results with the output of DENBStat4GSEA can also be used to run DEpermutePval.

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.

DENBStat4GSEA, runDESeq, DEpermutePval, genpermuteMat

data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
DEpermNBstat <- DENBStatPermut4GSEA(DEG, permuteMat) 
DEpermNBstat[1:10,1:10]