enrich.HGT: Do enrichment analysis using hypergeometric test

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

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", "Ensembl", 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 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"))

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