read_gmt: A function to read GMT file
In skimlab/CCSBUtils: R Utilitiy Functions for CCSB

read_gmt

R Documentation

A function to read GMT file

Description

A function to read GMT file

Usage

read_gmt(
  gmt.file,
  min.size = 1,
  max.size = -1,
  simplify = TRUE,
  sep1 = "\t",
  sep2 = sep1
)

Arguments

`gmt.file`	a text file in 'gmt' format.
`min.size`	The minimum gene set size to read. Defaults to 0.
`max.size`	The maximum gene set size to read. Defaults to no limit.
`simplify`	Defaults to TRUE. See 'output' for detail.
`sep1`	a character string separating 'gene set name', 'url' and 'gene set'
`sep2`	a character string separating each gene in 'gene set'

Value

a list of gene set. If TRUE, the return structure is simplified to a list of genesets each of which is a list of genes and the name of each geneset is the name of gene set from MSigDB file, the first element of each line. If FALSE, it returns a list of three element list each element of which is name, url, and geneset.

skimlab/CCSBUtils documentation built on March 30, 2022, 4:52 a.m.