Read a GMT-format gene set file — read

Parses a plain-text .gmt file (one gene set per line: set name, description, then tab-separated gene identifiers - the format used by MSigDB and similar resources) into a named list of character vectors, one per gene set. Blank lines are ignored.

Usage

read_gmt(file)

Arguments

file: Path to a .gmt file

Value

A named list of character vectors of gene identifiers, one per gene set, named after the set name in the file's first column.

Examples

gmt_file <- tempfile(fileext = ".gmt")
writeLines(c(
  "SET1\tdescription\tGeneA\tGeneB\tGeneC",
  "SET2\tdescription\tGeneD\tGeneE"
), gmt_file)
read_gmt(gmt_file)
#> $SET1
#> [1] "GeneA" "GeneB" "GeneC"
#> 
#> $SET2
#> [1] "GeneD" "GeneE"
#>