Example gene sets defined from the CPDB database

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Description

This list data object contains 25 gene sets defined from the CPDB database and is used for testing purposes.

Usage

1
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

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  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]])