exgensets {bc3net} | R Documentation |
Example gene sets defined from the CPDB database
Description
This list data object contains 25 gene sets defined from the CPDB database and is used for testing purposes.
Usage
data(exgensets)
Format
A list object with 25 character vectors.
Details
An list object of 25 pathway gene sets from CPDB with gene symbols.
Source
http://consensuspathdb.org/
References
A. Kamburov, U. Stelzl, H. Lehrach and R. Herwig, The ConsensusPathDB interaction database: 2013 update, Nucleic Acids Research, Volume 41, Issue D1, Pp. D793-D800
Examples
data(exgensets)
# The gene set collection from CPDB can be formatted by:
# "CPDB_pathways_genes.tab" is available in the download section in http://consensuspathdb.org/
# cpdb = readLines("CPDB_pathways_genes.tab", warn = FALSE)
# cpdb = lapply(cpdb, function(x) strsplit(x, "\t")[[1]])
# names(cpdb) = sapply(cpdb, function(x) paste(x[3], x[2], x[1], sep=":") )
# cpdb = lapply(cpdb, function(x) x[-c(1:3)])
# cpdb = cpdb[-length(cpdb)]
# cpdb = lapply(cpdb, function(x) strsplit(x, ",")[[1]])
[Package bc3net version 1.0.4 Index]