Description Usage Format Details Source References Examples
This list data object contains 25 gene sets defined from the CPDB database and is used for testing purposes.
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A list object with 25 character vectors.
An list object of 25 pathway gene sets from CPDB with gene symbols.
http://consensuspathdb.org/
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
1 2 3 4 5 6 7 8 9 10 | 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]])
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Loading required package: c3net
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: infotheo
Loading required package: Matrix
Loading required package: lattice
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