enrich.GSE: Gene set enrichment analysis

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

Description

A universal gene set enrichment analysis tools

Usage

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

Arguments

geneList	A order ranked numeric vector with geneid 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
gmtpath	The path to customized gmt file
by	One of 'fgsea' or 'DOSE'
verbose	Boolean
...	Other parameter

Value

An enrichResult instance

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.ORT

EnrichAnalyzer

gseGO

gseKEGG

GSEA

enrichResult-class

Examples

data(geneList, package = "DOSE")
## Not run: 
    enrichRes = enrich.GSE(geneList, keytype = "entrez")
    head(slot(enrichRes, "result"))

## End(Not run)

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