DSpermutePval {SeqGSEA} | R Documentation |
Calculate permutation p-values in differential splicing analysis.
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
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))