topGeneSets: Extract top significant gene sets

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

This function is to extract n top significant gene sets overrepresented in the samples studied, ranked by FDR, p-values, or FWER.

Usage

topGeneSets(gene.set, n = 20, sortBy = c("FDR", "pvalue", "FWER"), GSDesc = FALSE)

Arguments

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.

Value

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.

Author(s)

Xi Wang, [e-mail]

See Also

GSEnrichAnalyze, GSEAresultTable

Examples

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)

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.