WikiPathways_GeneSet_R

Shell/R scripts to import gene sets into R (compatible with safe::getCmatrix)

import_gene_set.R will load bioconductor packages for KEGG, Gene Ontology (GO), Reactome and call other scripts for WikiPathways: download_WikiPathways.sh (will run download_WikiPathways.R)

Files used for WikiPathways will be stored in subdirectory Human_WP, output RData files ready to load in current directory: either run scripts to update datasets from web or use existing RData files (last updated 23 June 2015)

Entrez gene IDs used to define gene sets (pathways): requires org.Hs.eg.db package to map to Gene Symbols

WikiPathway download can be modified by altering the wget <url> in download_WikiPathways.sh

• change Genus%20species as needed
• remove tags (as shown by commented out wget line)

Requires:

• any recent version of R
• access to bioconductore packages
• BASH (or and Unix shell)