gmt_to_list: convert gmt format of pathways to list of vectors

View source: R/utils.R

gmt_to_listR Documentation

convert gmt format of pathways to list of vectors

Description

convert gmt format of pathways to list of vectors

Usage

gmt_to_list(
  path,
  cutoff = 0,
  sep = "\thttp://www.broadinstitute.org/gsea/msigdb/cards/.*?\t"
)

Arguments

path

gmt file path

cutoff

remove pathways with less genes than this cutoff

sep

sep used in file to split path and genes

Value

list of genes in each pathway

Examples

gmt_file <- system.file(
    "extdata",
    "c2.cp.reactome.v6.2.symbols.gmt.gz",
    package = "clustifyr"
)

gl <- gmt_to_list(path = gmt_file)
length(gl)

NCBI-Hackathons/RClusterCT documentation built on July 10, 2022, 6:18 a.m.