exgensets: Example gene sets defined from the CPDB database

Description Usage Format Details Source References Examples

Description

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

Usage

1

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]])

Example output

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

bc3net documentation built on May 30, 2017, 5:22 a.m.