## ----style, echo = FALSE, results = 'asis', message=FALSE--------------------- BiocStyle::markdown() ## ----load-lib, message = FALSE------------------------------------------------ library(AnnotationHub) ah <- AnnotationHub() ## ----list-wikipathwaysdb------------------------------------------------------ query(ah, "wikipathways") ## ----confirm-metadata--------------------------------------------------------- mcols(query(ah, "wikipathways")) ## ----query-hsa---------------------------------------------------------------- qr <- query(ah, c("wikipathways", "Homo sapiens")) qr ## ----load-hsatbl-------------------------------------------------------------- hsatbl <- qr[[1]] hsatbl ## ----get-metabolites---------------------------------------------------------- hsatbl[hsatbl$`pathway_name`=="Amino Acid metabolism", ] ## ----create-rda, eval = FALSE------------------------------------------------- # library(AHWikipathwaysDbs) # scr <- system.file("scripts/make-data.R", package = "AHWikipathwaysDbs") # source(scr) # createWikipathwaysMetabolitesDb()