DEpermutePval {SeqGSEA} | R Documentation |
Calculate permutation p-values in differential expression analysis for each genes.
DEpermutePval(DEGres, permuteNBstat)
DEGres |
the output of |
permuteNBstat |
the output of |
A data frame containing the expression means and variances for each gene in each group compared, and NB-stats, permutation p-values and adjusted p-values for each gene.
Xi Wang, xi.wang@newcastle.edu.au
runDESeq
,
DENBStat4GSEA
,
DENBStatPermut4GSEA
,
DENBTest
data(RCS_example, package="SeqGSEA") permuteMat <- genpermuteMat(RCS_example, times=10) geneCounts <- getGeneCount(RCS_example) label <- label(RCS_example) DEG <- runDESeq(geneCounts, label) DEGres <- DENBStat4GSEA(DEG) DEpermNBstat <- DENBStatPermut4GSEA(DEG, permuteMat) DEGres <- DEpermutePval(DEGres, DEpermNBstat) head(DEGres)