DENBStatPermut4GSEA {SeqGSEA} | R Documentation |
Calculate NB-statistics quantifying differential expression for each gene in the permutation data sets. The results will be used for GSEA run.
DENBStatPermut4GSEA(DEG, permuteMat)
DEG |
a CountDataSet object, can be the output of |
permuteMat |
a permutation matrix generated by |
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]