Pathway and Gene Ontology enrichment
User needs to adjsut settings at top of code (line 20-60).
******************** N.B Check KEGG terms if commercial user. ****************************
Code to determine enriched Gene Ontology and Pathways using KEGG and Reactome using hypergeometric tests. Input: list of ids of type specified in code. Outputs: Gene Ontology (Enrichment using GOstats) Tables GO enriched terms GO.BP.table, GO.CC.table, GO.MF.table for "Biological Process", "Cellular Component" and "Molecular Function" respectively Figures of enriched terms for upto 10 most significant groups. x axis = -log10 pvalue, number of IDs in term shown by size and colour of circle.
KEGG (using gage and pathview) enriched pathways table (KEGG.enrichment.analysis.results.table) pathview output e.g mmu03010.pathview.png: shows entities in user input list which are present in enriched pathway
GO and KEGG tables are combined into a single excel sheet for simple reporting. NIPA.report.txt: Any errors will appear here.