## ----style, echo = FALSE, results = 'asis', message=FALSE--------------------- BiocStyle::markdown() ## ----load-lib, message = FALSE------------------------------------------------ library(AnnotationHub) ah <- AnnotationHub() ## ----list-pathbankdb---------------------------------------------------------- query(ah, "pathbank") ## ----confirm-metadata--------------------------------------------------------- mcols(query(ah, "pathbank")) ## ----query-ecoli-------------------------------------------------------------- qr <- query(ah, c("pathbank", "Escherichia coli")) qr ## ----load-ecolitbl------------------------------------------------------------ ecolitbl <- qr[[1]] ecolitbl ## ----get-metabolites4TCA------------------------------------------------------ ecolitbl[ecolitbl$`Pathway Name`=="TCA Cycle", ] ## ----create-rda, eval = FALSE------------------------------------------------- # library(AHPathbankDbs) # scr <- system.file("scripts/make-data.R", package = "AHPathBankDbs") # source(scr) # createPathbankMetabolitesDb() # createPathbankProteinsDb()