read_msigdb: Read files from my MSigDB cache

In ChristopherBarrington/helpr: Tools To Make R Life Easier

Read files from my MSigDB cache

Description

Reads an MSigDB gmt file and returns a list of genes in pathways.

Usage

read_msigdb(
  collection = "h.all",
  pathways = NULL,
  version = "7.4",
  identifier = "symbols",
  dbroot = "/camp/stp/babs/working/barrinc/db/msigdb"
)

Arguments

collection	Name of the collection
pathways	Character vector of pathways in collection to keep
version	Release version
identifier	Identifier type: symbols or entrez (entrez may not exist!!)
dbroot	Path to the root of the MSigDB files

Value

A list of genes in pathways, with pathway name as the key and a character vector of gene identifiers (identifer).

ChristopherBarrington/helpr documentation built on Oct. 25, 2024, 9:17 a.m.