Calculate NB-statistics quantifying DE for each gene in the permutation data sets

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Description

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

Usage

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DENBStatPermut4GSEA(DEG, permuteMat)

Arguments

DEG

a CountDataSet 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, xi.wang@newcastle.edu.au

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

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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]

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