DEpermutePval {SeqGSEA} | R Documentation

## Permutation for p-values in differential expression analysis

### 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, xi.wang@newcastle.edu.au

### 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)

[Package SeqGSEA version 1.20.0 Index]