enrich.ORT: Enrichment analysis using over-representation test

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Enrichment analysis using over-representation test

Description

Enrichment analysis using over-representation test

Usage

enrich.ORT(
  geneList,
  keytype = "Symbol",
  type = "GOBP",
  organism = "hsa",
  pvalueCutoff = 1,
  limit = c(2, 100),
  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

Examples

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

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.