gsGetter {MAGeCKFlute} | R Documentation

## Extract pathway annotation from GMT file.

### Description

Extract pathway annotation from GMT file.

### Usage

    gsGetter(gmtpath = NA, type = "All", limit = c(0, Inf),
      organism = "hsa")

### Arguments

`gmtpath` | The path to customized gmt file.
`type` | Geneset category for testing.
`limit` | A two-length vector (default: c(3, 50)), specifying the minimal and maximal size of gene sets for enrichent analysis.
`organism` | 'hsa' or 'mmu'.

### Value

A three-column data frame.

### Author(s)

Wubing Zhang

### Examples

    gene2path = gsGetter()
    head(gene2path)

[Package MAGeCKFlute version 1.4.3 Index]