topDSExons {SeqGSEA} | R Documentation |
This function is to extract top n differentially spliced exons, ranked by p-values or NB-stats.
topDSExons(RCS, n = 20, sortBy = c("pvalue", "NBstat"))
RCS |
a ReadCountSet object after running |
n |
the number of top genes. |
sortBy |
indicating whether p-value or NBstat to be used for ranking genes. |
A table for top n exons. Columns include: geneID, exonID, testable, NBstat, pvalue, padjust, and meanCounts.
Xi Wang, xi.wang@newcastle.edu.au
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) topDSExons(RCS_example, 10, "NB")