The function will map the genes in KEGG pathway database, and then hypergegeometric tests would be used to estimate the significance of enrichment for each pathway
the species id in KEGG database, 'hsa' means human, 'mmu' means mouse, 'rno' means rat, etc
returned_pvalue
the minimum p value for enriched pathways
returned_adjpvalue
the minimum adjusted p value for enriched pathways
returned_genenumber
the minimum number of annotated genes for enriched pathways
download_latest
logical. Indicate if the function will download the latest pathway/gene link from KEGG website. As the KEGG.db package was not updated for a long time due to the KEGG policy change, we provided this parameter so that the users could get the latest KEGG database.
Value
a list with two parts
name stastic
description a matirx containing the pathway IDs of enriched pathways, and their names, p values, number of annotated genes
name detail
description a list with the genes annotated for each pathway
Details
Only the pathways with p value <= returned_pvalue="" in="" hypergegeometric="" tests="" and="" number="" of="" annotated="" genes="">= returned_genenumber would be taken as enriched and returned.
data(pho_sites_count)
#the 300 genes with most phospholation sites quantifiedgenes<-names(rev(sort(pho_sites_count[,1]))[1:300])
pho_KEGGresult<-find_enriched_pathway(genes,species='hsa')