DENBStatPermut4GSEA: Calculate NB-statistics quantifying DE for each gene in the...

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

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

Usage

DENBStatPermut4GSEA(dds, permuteMat)

Arguments

dds	a DESeqDataSet object, can be the output of runDESeq.
permuteMat	a permutation matrix generated by genpermuteMat.

Value

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

Note

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

Author(s)

Xi Wang, [e-mail]

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

DENBStat4GSEA, runDESeq, DEpermutePval, genpermuteMat

Examples

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

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.