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]