EnrichAnalyzer: Enrichment analysis

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

Enrichment analysis

Description

Enrichment analysis

Usage

EnrichAnalyzer(
  geneList,
  keytype = "Symbol",
  type = "Pathway+GOBP",
  method = "HGT",
  organism = "hsa",
  pvalueCutoff = 1,
  limit = c(2, 100),
  universe = NULL,
  filter = FALSE,
  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').
method	One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test).
organism	'hsa' or 'mmu'.
pvalueCutoff	FDR cutoff.
limit	A two-length vector (default: c(2, 200)), specifying the minimal and maximal size of gene sets for enrichent analysis.
universe	A character vector, specifying the backgound genelist, default is whole genome.
filter	Boolean, specifying whether filter out redundancies from the enrichment results.
gmtpath	The path to customized gmt file.
verbose	Boolean

Value

enrichRes is an enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.GSE

enrich.ORT

enrich.HGT

enrichResult-class

Examples

data(geneList, package = "DOSE")
## Not run: 
  keggA = EnrichAnalyzer(geneList[1:500], keytype = "entrez")
  head(keggA@result)

## End(Not run)

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