read_gene_sets: read_gene_sets

In biodataganache/leapR: Layered enrichment analysis of pathways R

read_gene_sets

Description

read_gene_sets is a function to import external pathway database files in .gmt format

Usage

read_gene_sets(
  gsfile,
  gene.labels = NA,
  gs.size.threshold.min = 5,
  gs.size.threshold.max = 15000
)

Arguments

gsfile	is a gene set file, for example a .gmt file (gene matrix transposed file format)
gene.labels	defaults to NA
gs.size.threshold.min	defaults to 5
gs.size.threshold.max	defaults to 15000

Value

gene set object

geneset list

Examples

gfile = system.file('extdata','h.all.v2024.1.Hs.symbols.gmt',package='leapR')
glist = read_gene_sets(gfile)

biodataganache/leapR documentation built on July 16, 2025, 11:10 p.m.