Compute NB-statistics quantifying differential splicing on the permutation data set.

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Description

This function is to calculate NB-statistics quantifying differential splicing for each gene on each permutation data set. The results will be used for GSEA run as DS background.

Usage

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DSpermute4GSEA(RCS, permuteMat)

Arguments

RCS

a ReadCountSet object after running exonTestability.

permuteMat

a permutation matrix generated by genpermuteMat.

Details

Parallel running configuration: TODO

Value

A ReadCountSet object with slot permute_NBstat_gene updated.

Note

Please run exonTestability before run this function.

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

exonTestability, genpermuteMat, DENBStatPermut4GSEA, DSpermutePval

Examples

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data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
RCS_example <- exonTestability(RCS_example)
RCS_example <- DSpermute4GSEA(RCS_example, permuteMat)
head(RCS_example@permute_NBstat_gene)

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