fetchPathwayDefinitions: fetch pathway definitions from downloads.baderlab.org
In netDx: Network-based patient classifier
Description
Usage
Arguments
Details
Value
Examples
Description
fetch pathway definitions from downloads.baderlab.org
Usage
1
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
1
2
3
fetchPathwayDefinitions("October",2020)
fetchPathwayDefinitions("January",2018)
fetchPathwayDefinitions(month=10,year=2020)
netDx documentation built on Dec. 11, 2020, 2:01 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Examples
Description
fetch pathway definitions from downloads.baderlab.org
Usage
1 | 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
1 2 3 | fetchPathwayDefinitions("October",2020)
fetchPathwayDefinitions("January",2018)
fetchPathwayDefinitions(month=10,year=2020)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.