enrich.GOstats {MAGeCKFlute}R Documentation

Do enrichment analysis using GOstats

Description

Do enrichment analysis using GOstats method

Usage

enrich.GOstats(gene, universe = NULL, type = c("KEGG", "BP", "MF", "CC"),
  organism = "hsa", pvalueCutoff = 0.25, pAdjustMethod = "BH")

Arguments

gene

A character vector, specifying the genelist to do enrichment analysis.

universe

A character vector, specifying the backgound genelist, default is whole genome.

type

Geneset category for testing, KEGG(default).

organism

A character, specifying organism, such as "hsa" or "Human"(default), and "mmu" or "Mouse"

pvalueCutoff

Pvalue cutoff.

pAdjustMethod

One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.DAVID

enrich.GSE

enrich.ORT

enrichment_analysis

enrichResult-class

Examples

data(geneList, package = "DOSE")
genes <- names(geneList)[1:100]
## Not run: 
    enrichRes <- enrich.GOstats(genes, type="BP")
    head(enrichRes@result)

## End(Not run)


[Package MAGeCKFlute version 1.0.1 Index]