In jhrcook/readgmt: Read GMT gene set files from MSigDB

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

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))
head(kegg$KEGG_COLORECTAL_CANCER)

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)

# convert from list format to tibble
tidy_gmt(kegg)

jhrcook/readgmt documentation built on Oct. 21, 2019, 7:51 p.m.