writeSigGeneSet: Write gene set supporting information

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

Description

This function is to write the specified gene set (whose index is i) with significance information, including p-value and FDR, and gene scores for each gene in this set.

Usage

writeSigGeneSet(gene.set, i, gene.score, file = "")

Arguments

gene.set	an object of class SeqGeneSet with GSEnrichAnalyze done.
i	the i-th gene set in the SeqGeneSet object. topGeneSets is useful to find the most significantly overrepresented gene set.
gene.score	the vector of gene scores for running GSEA.
file	output file name, if not specified print to screen.

Details

See plotSigGeneSet, which shows graphic information of the gene set specified.

Author(s)

Xi Wang, [e-mail]

See Also

GSEnrichAnalyze, topGeneSets, plotSigGeneSet

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)
writeSigGeneSet(GS_example, 9, gene.score) # 9th gene set is the most significant one.

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.