* Description
This program allows to perform gene-set analyses with the results of the Connectivity Map project. Please see the CMAP
project website for details of its nature www.broadinstitute.org/cmap/.
See https://github.com/inti/CMAP_GSA/wiki for additional details.
* BUGS and questions
In case of bugs or question please e-mail Inti Pedroso <intipedroso@gmail.com> or Gerome Breen <gerome.breen@gmail.com>
* Files in the distribution
README = this readme fiel
cmap_gsa.R = main R script to perform analyses
data: folder with data files
- trials_4_cmap_drugs.txt = table with constructec with the clinicaltrials.gov data base with drug for each diseases. It provides the phase of the clinical trial as well as the name of the diease and drug.
- CMAP.RData = R compressed binary data with the fold-change, log fold-change and averaged log fold-change values for each drug.
example: folder with example files
- gwascatalog_10_december_2010.txt = genes mapped to genome-wide significant SNPs (i.e. with p-values < 5x10-8) reported on the GWAS Catalogue (www.genome.gov/gwastudies) as of 10th of December, 2010.
- wtcc1_gene_sets.txt = significant gene-sets from the re-analysis of the WTCCC1 GWAS performed with the FORGE software by Pedroso et al (unpublished)
- wtcc1_genes.txt = as above but sinificant genes.
- wtcc1_snps.txt = genome-wide significant SNPs reported by the WTCCC1.