DEpermutePval: Permutation for p-values in differential expression analysis

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

Description

Calculate permutation p-values in differential expression analysis for each genes.

Usage

DEpermutePval(DEGres, permuteNBstat)

Arguments

DEGres	the output of DENBStat4GSEA.
permuteNBstat	the output of DENBStatPermut4GSEA.

Value

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.

Author(s)

Xi Wang, [e-mail]

See Also

runDESeq, DENBStat4GSEA, DENBStatPermut4GSEA, DENBTest

Examples

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)

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