enrich.HGT {MAGeCKFlute}R Documentation

Do enrichment analysis using Hypergeometric test

Description

Do enrichment analysis using Hypergeometric test

Usage

enrich.HGT(
  geneList,
  keytype = "Symbol",
  type = "GOBP",
  organism = "hsa",
  pvalueCutoff = 0.25,
  limit = c(2, 200),
  universe = NULL,
  gmtpath = NULL,
  verbose = TRUE
)

Arguments

geneList

A numeric vector with gene as names.

keytype

"Entrez" or "Symbol".

type

Molecular signatures for testing, available datasets include Pathway (KEGG, REACTOME, C2_CP), GO (GOBP, GOCC, GOMF), MSIGDB (C1, C2 (C2_CP (C2_CP_PID, C2_CP_BIOCARTA), C2_CGP), C3 (C3_MIR, C3_TFT), C4, C6, C7, HALLMARK) and Complex (CORUM). Any combination of them are also accessible (e.g. 'GOBP+GOMF+KEGG+REACTOME').

organism

'hsa' or 'mmu'.

pvalueCutoff

Pvalue cutoff.

limit

A two-length vector, 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.

verbose

Boolean

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.GSE

enrich.ORT

EnrichAnalyzer

enrichResult-class

Examples

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


[Package MAGeCKFlute version 1.8.0 Index]