readgmt

The goal of ‘readgmt’ is to easily import a GMT file from MSigDB as a list of gene sets.

See the full documentation here: jhrcook.github.io/readgmt

Installation

This package is not available on CRAN (it is much too simple for that), so it must be installed from GitHub with

devtools::install_github("jhrcook/readgmt")

Example

Here is an example of reading in the KEGG gene set (downloaded on 2019/04/01).

library(readgmt)
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"

This can also be read in as a “tidy” tibble, or converted after the reading it in as a list.

# read in as a tibble
read_gmt(kegg_path, tidy = TRUE)
#> # A tibble: 12,875 x 2
#>    gene_set                        gene 
#>    <chr>                           <chr>
#>  1 KEGG_GLYCOLYSIS_GLUCONEOGENESIS ACSS2
#>  2 KEGG_GLYCOLYSIS_GLUCONEOGENESIS GCK  
#>  3 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PGK2 
#>  4 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PGK1 
#>  5 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PDHB 
#>  6 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PDHA1
#>  7 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PDHA2
#>  8 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PGM2 
#>  9 KEGG_GLYCOLYSIS_GLUCONEOGENESIS TPI1 
#> 10 KEGG_GLYCOLYSIS_GLUCONEOGENESIS ACSS1
#> # … with 12,865 more rows

# convert from list format to tibble
tidy_gmt(kegg)
#> # A tibble: 12,875 x 2
#>    gene_set                        gene 
#>    <chr>                           <chr>
#>  1 KEGG_GLYCOLYSIS_GLUCONEOGENESIS ACSS2
#>  2 KEGG_GLYCOLYSIS_GLUCONEOGENESIS GCK  
#>  3 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PGK2 
#>  4 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PGK1 
#>  5 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PDHB 
#>  6 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PDHA1
#>  7 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PDHA2
#>  8 KEGG_GLYCOLYSIS_GLUCONEOGENESIS PGM2 
#>  9 KEGG_GLYCOLYSIS_GLUCONEOGENESIS TPI1 
#> 10 KEGG_GLYCOLYSIS_GLUCONEOGENESIS ACSS1
#> # … with 12,865 more rows