# Calculate NB-statistics quantifying DE for each gene in the permutation data sets

### Description

Calculate NB-statistics quantifying differential expression for each gene in the permutation data sets. The results will be used for GSEA run.

### Usage

1 | ```
DENBStatPermut4GSEA(DEG, permuteMat)
``` |

### Arguments

`DEG` |
a CountDataSet object, can be the output of |

`permuteMat` |
a permutation matrix generated by |

### Value

A matrix of NB-statistics. Each row corresponds to each gene, and each column to each permutation.

### Note

The results with the output of `DENBStat4GSEA`

can also be used to run `DEpermutePval`

.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### References

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.

### See Also

`DENBStat4GSEA`

,
`runDESeq`

,
`DEpermutePval`

,
`genpermuteMat`

### Examples

1 2 3 4 5 6 7 | ```
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]
``` |