topGeneSets {SeqGSEA} | R Documentation |
This function is to extract n top significant gene sets overrepresented in the samples studied, ranked by FDR, p-values, or FWER.
topGeneSets(gene.set, n = 20, sortBy = c("FDR", "pvalue", "FWER"), GSDesc = FALSE)
gene.set |
an object of class SeqGeneSet after GSEA runs. |
n |
the number of top gene sets. |
sortBy |
indicating which method to rank gene sets. |
GSDesc |
logical indicating whether or not to output gene set descriptions. |
A data frame for top n gene sets detected with respect to the ranking method specified. Information includes: GSName, GSSize, ES, ES.pos, pval, FDR, and FWER.
Xi Wang, xi.wang@newcastle.edu.au
GSEnrichAnalyze
,
GSEAresultTable
data(DEscore, package="SeqGSEA") data(DSscore, package="SeqGSEA") gene.score <- geneScore(DEscore, DSscore, method="linear", DEweight = 0.3) data(DEscore.perm, package="SeqGSEA") data(DSscore.perm, package="SeqGSEA") gene.score.perm <- genePermuteScore(DEscore.perm, DSscore.perm, method="linear", DEweight=0.3) data(GS_example, package="SeqGSEA") GS_example <- GSEnrichAnalyze(GS_example, gene.score, gene.score.perm) topGeneSets(GS_example, n=5)