gsGetter {MAGeCKFlute} | R Documentation

## Extract pathway annotation from GMT file.

### Description

Extract pathway annotation from GMT file.

### Usage

    gsGetter(
      gmtpath = NULL,
      type = "All",
      limit = c(0, Inf),
      organism = "hsa",
      update = FALSE
    )

### Arguments

`gmtpath` | The path to customized gmt file.
`type` | Molecular signatures for testing, available datasets include Pathway (KEGG, REACTOME, C2_CP:PID, C2_CP:BIOCARTA), GO (GOBP, GOCC, GOMF), MSIGDB (C1, C2 (C2_CP (C2_CP:PID, C2_CP:BIOCARTA), C2_CGP), C3 (C3_MIR, C3_TFT), C4 (C4_CGN, C4_CM), C5 (C5_BP, C5_CC, C5_MF), C6, C7, H) and Complex (CORUM). Any combination of them are also accessible (e.g. 'GOBP+GOMF+KEGG+REACTOME').
`limit` | A two-length vector, specifying the minimal and maximal size of gene sets to load.
`organism` | 'hsa' or 'mmu'.
`update` | Boolean, indicating whether update the gene sets from source database.

### Value

A three-column data frame.

### Author(s)

Wubing Zhang

### Examples

    gene2path = gsGetter(type = "REACTOME+KEGG")
    head(gene2path)

[Package MAGeCKFlute version 1.12.0 Index]