Read a GMT file from MSigDB

Reads a GMT file containing a gene set from MSigDB and returns a list of named gene sets

read_gmt(file, tidy = FALSE)

Arguments

file	path to the downloaded GMT file
tidy	turn into a tidy tibble with tidy_gmt

Value

returns a named list of the gene set

Examples

kegg_path <- system.file("extdata", "c2.cp.kegg.v6.2.symbols.gmt.txt",
                         package = "readgmt")
kegg <- read_gmt(kegg_path)
head(names(kegg))
#> [1] "KEGG_GLYCOLYSIS_GLUCONEOGENESIS"              
#> [2] "KEGG_CITRATE_CYCLE_TCA_CYCLE"                 
#> [3] "KEGG_PENTOSE_PHOSPHATE_PATHWAY"               
#> [4] "KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS"
#> [5] "KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM"         
#> [6] "KEGG_GALACTOSE_METABOLISM"                    
head(kegg$KEGG_COLORECTAL_CANCER)
#> [1] "JUN"   "CASP9" "RAF1"  "BIRC5" "APC2"  "RHOA"