enrich.HGT {MAGeCKFlute}R Documentation

Do enrichment analysis using Hypergeometric test

Description

Do enrichment analysis using Hypergeometric test

Usage

enrich.HGT(gene, universe = NULL, type = "KEGG", organism = "hsa",
  pvalueCutoff = 0.25, pAdjustMethod = "BH", minGSSize = 2,
  maxGSSize = 500)

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".

minGSSize

Minimal size of each geneSet for testing.

maxGSSize

Maximal size of each geneSet for analyzing.

Value

A enrichResult instance.

Author(s)

Feizhen Wu

See Also

enrich.GOstats

enrich.DAVID

enrich.GSE

enrich.ORT

enrichment_analysis

enrichResult-class

Examples

data(geneList, package = "DOSE")
genes <- names(geneList)[1:100]
enrichRes <- enrich.HGT(genes)
head(enrichRes@result)


[Package MAGeCKFlute version 1.0.1 Index]