# Permutation for p-values in differential expression analysis

### Description

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

### Usage

1 | ```
DEpermutePval(DEGres, permuteNBstat)
``` |

### Arguments

`DEGres` |
the output of |

`permuteNBstat` |
the output of |

### 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

1 2 3 4 5 6 7 8 9 | ```
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)
``` |

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