enrich.GSE {MAGeCKFlute} | R Documentation

## Gene set enrichment analysis

### 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)

[Package MAGeCKFlute version 1.12.0 Index]