Calculate permutation p-values in differential splicing analysis.

1 | ```
DSpermutePval(RCS, permuteMat)
``` |

`RCS` |
a ReadCountSet object after running |

`permuteMat` |
a permutation matrix generated by |

Permutation p-values are computed based on NB-statistics for comparison of the studied groups and NB-statistics from the permutation data sets.

A ReadCountSet object with slots `permute_NBstat_exon`

, `permute_NBstat_gene`

, `featureData`

, and `featureData_gene`

updated.

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

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.

`estiExonNBstat`

,
`estiGeneNBstat`

,
`genpermuteMat`

,
`DSpermute4GSEA`

1 2 3 4 5 6 7 8 | ```
data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
RCS_example <- exonTestability(RCS_example)
RCS_example <- estiExonNBstat(RCS_example)
RCS_example <- estiGeneNBstat(RCS_example)
RCS_example <- DSpermutePval(RCS_example, permuteMat)
head(DSresultExonTable(RCS_example))
head(DSresultGeneTable(RCS_example))
``` |

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