gmt_to_list: convert gmt format of pathways to list of vectors

In NCBI-Hackathons/clustifyR: Classifier for Single-cell RNA-seq Using Cell Clusters

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"
)

gene.lists <- gmt_to_list(path = gmt_file)
length(gene.lists)

NCBI-Hackathons/clustifyR documentation built on Aug. 31, 2024, 5:35 a.m.