## ----setu,echo=FALSE,results="hide"-------------------------------------- suppressMessages({ suppressPackageStartupMessages({ library(hmdbQuery) library(gwascat) }) }) ## ----lk1----------------------------------------------------------------- library(hmdbQuery) lk1 = HmdbEntry(prefix = "http://www.hmdb.ca/metabolites/", id = "HMDB0000001") ## ----lk2----------------------------------------------------------------- lk1 ## ----lkta---------------------------------------------------------------- data(hmdb_disease) hmdb_disease ## ----lkdis3-------------------------------------------------------------- diseases(lk1) pmids = unlist(diseases(lk1)[1,]$pmids) library(annotate) pm = pubmed(pmids[1]) ab = buildPubMedAbst(xmlRoot(pm)[[1]]) ab ## ----lkdee--------------------------------------------------------------- biospecimens(lk1) tissues(lk1) st = store(lk1) head(names(st)) length(names(st)) sapply(store(lk1)$protein_associations, "[[", "name") sapply(store(lk1)$protein_associations, "[[", "gene_name")