fetchPathwayDefinitions {netDx}R Documentation

fetch pathway definitions from downloads.baderlab.org

Description

fetch pathway definitions from downloads.baderlab.org

Usage

fetchPathwayDefinitions(month = NULL, year = NULL, verbose = FALSE)

Arguments

month

(char) month of pathway definition file. Must be textual name (e.g. "January","April"). If NULL, gets the latest release

year

(numeric) year of pathway definition file. Must be in yyyy format (e.g. 2018).

verbose

(logical) print messages

Details

Fetches genesets compiled from multiple curated pathway databases. Downloaded from: http://download.baderlab.org/EM_Genesets/ The file contains pathways from HumanCyc, NetPath, Reactome, NCI Curated Pathways and mSigDB. For details see Merico D, Isserlin R, Stueker O, Emili A and GD Bader. (2010). PLoS One. 5(11):e13984.

Value

(char) Path to local cached copy of GMT file or initial download is required

Examples

fetchPathwayDefinitions()
fetchPathwayDefinitions("January",2018)
fetchPathwayDefinitions()

[Package netDx version 1.0.3 Index]