fetchPathwayDefinitions: fetch pathway definitions from downloads.baderlab.org

Description Usage Arguments Details Value Examples

View source: R/fileCache.R

Description

fetch pathway definitions from downloads.baderlab.org

Usage

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fetchPathwayDefinitions(month = NULL, year = NULL, day = 1, verbose = FALSE)

Arguments

month

(numeric or char) month of pathway definition file. Can be numeric or text (e.g. "January","April"). If NULL, fails.

year

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

day

(integer)

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

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fetchPathwayDefinitions("October",2020)
fetchPathwayDefinitions("January",2018)
fetchPathwayDefinitions(month=10,year=2020)

netDx documentation built on Dec. 11, 2020, 2:01 a.m.