## ----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------------------------------------------------------------------- d1 = diseases(lk1) # matrix pmids = unlist(d1[3,1][[1]]["pubmed_id",]) 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)) st$protein_assoc["name",] st$protein_assoc["gene_name",]