plotSigGeneSet: Plot gene set details

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

Description

This function is to generate a two-panel plot showing detailed information of the gene set specified. One panel is showing the running enrichment scores and the position where the ES appear. The other panel shows the significance level of the ES, comparing with permutation ESs.

Usage

plotSigGeneSet(gene.set, i, gene.score, pdf = NULL)

Arguments

gene.set	a SeqGeneSet object after running GSEnrichAnalyze.
i	the i-th gene set in the SeqGeneSet object. topGeneSets is useful to find the most significantly overrepresented gene set.
gene.score	the gene score vector containing gene scores for each gene.
pdf	whether to save the plot to PDF file; if yes, provide the name of the PDF file.

Details

See writeSigGeneSet, which writes the detailed gene set information to a file or to the screen.

Author(s)

Xi Wang, [e-mail]

See Also

GSEnrichAnalyze, topGeneSets, plotSig, plotES, writeSigGeneSet

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)
plotSigGeneSet(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.