SeqGSEA (version 1.12.0)

writeSigGeneSet: Write gene set supporting information

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.

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.