convert gmt format of pathways to list of vectors — gmt_to_list • clustifyr

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"
)

gene.lists <- gmt_to_list(path = gmt_file)
length(gene.lists)
#> [1] 674