enrich.HGT {MAGeCKFlute}R Documentation

Do enrichment analysis using Hypergeometric test

Description

Do enrichment analysis using Hypergeometric test

Usage

enrich.HGT(geneList, keytype = "Entrez", type = "CORUM",
  organism = "hsa", pvalueCutoff = 0.05, pAdjustMethod = "BH",
  limit = c(3, 50), universe = NULL, gmtpath = NA)

Arguments

geneList

A numeric vector with gene as names.

keytype

"Entrez" or "Symbol".

type

Geneset category for testing, one of 'CORUM', 'CPX' (ComplexPortal), 'GOBP', 'GOMF', 'GOCC', 'KEGG', 'BIOCARTA', 'REACTOME', 'WikiPathways', 'EHMN', 'PID', or any combination of them (e.g. 'GOBP+GOMF+CORUM'), or 'All' (all categories).

organism

'hsa' or 'mmu'.

pvalueCutoff

Pvalue cutoff.

pAdjustMethod

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

limit

A two-length vector (default: c(3, 50)), specifying the minimal and maximal size of gene sets for enrichent analysis.

universe

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

gmtpath

The path to customized gmt file.

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.GSE

enrich.ORT

enrichment_analysis

enrichResult-class

Examples

data(geneList, package = "DOSE")
genes <- geneList[1:300]
enrichRes <- enrich.HGT(genes, type = "KEGG", )
head(slot(enrichRes, "result"))


[Package MAGeCKFlute version 1.2.3 Index]