gmt_to_list: convert gmt format of pathways to list of vectors

Description Usage Arguments Value Examples

View source: R/utils.R

Description

convert gmt format of pathways to list of vectors

Usage

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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

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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 20, 2021, 3:15 p.m.