writeSigGeneSet {SeqGSEA} | R Documentation

## 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.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### 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.

[Package SeqGSEA version 1.34.0 Index]