enrich.ORT: Do enrichment analysis using over-representation test

Description Usage Arguments Value Author(s) See Also Examples

View source: R/enrich.ORT.R

Description

Do enrichment analysis using over-representation test

Usage

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enrich.ORT(
  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

FDR 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

...

Other parameter

Value

An enrichedResult instance.

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.GSE

EnrichAnalyzer

enrichGO

enrichKEGG

enricher

enrichResult-class

Examples

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data(geneList, package = "DOSE")
genes <- geneList[1:100]
enrichedRes <- enrich.ORT(genes, keytype = "entrez")
head(slot(enrichedRes, "result"))

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.