DSpermute4GSEA {SeqGSEA} | R Documentation |
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.
DSpermute4GSEA(RCS, permuteMat)
RCS |
a ReadCountSet object after running |
permuteMat |
a permutation matrix generated by |
Parallel running configuration: TODO
A ReadCountSet object with slot permute_NBstat_gene updated.
Please run exonTestability
before run this function.
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.
exonTestability
,
genpermuteMat
,
DENBStatPermut4GSEA
,
DSpermutePval
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)