## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install('biodbHmdb') ## ----results='hide'----------------------------------------------------------- mybiodb <- biodb::newInst() ## ----------------------------------------------------------------------------- conn <- mybiodb$getFactory()$createConn('hmdb.metabolites') ## ----------------------------------------------------------------------------- dbExtract <- system.file("extdata", 'generated', "hmdb_extract.zip", package="biodbHmdb") conn$setPropValSlot('urls', 'db.zip.url', dbExtract) ## ----------------------------------------------------------------------------- conn$getNbEntries() ## ----------------------------------------------------------------------------- ids <- conn$getEntryIds(2) ids ## ----------------------------------------------------------------------------- entries <- conn$getEntry(ids) entries ## ----------------------------------------------------------------------------- x <- mybiodb$entriesToDataframe(entries, compute=FALSE) x ## ----------------------------------------------------------------------------- id <- conn$searchForEntries(list(name='1-Methylhistidine'), max.results=1) id ## ----------------------------------------------------------------------------- conn$searchForEntries(list(name=c('propanoic', 'acid')), max.results=1) ## ----------------------------------------------------------------------------- entryDf <- conn$getEntry(id)$getFieldsAsDataframe(fields=c('accession', 'name')) ## ----entryByNameTable, echo=FALSE, results='asis'----------------------------- knitr::kable(entryDf, "pipe", caption="The entry returned when searching by name.") ## ----------------------------------------------------------------------------- id <- conn$searchForEntries(list(description=c('Parkinson', 'sclerosis')), max.results=1) id ## ----------------------------------------------------------------------------- entryDf <- conn$getEntry(id)$getFieldsAsDataframe(fields=c('accession', 'name', 'description')) ## ----entryByDescTable, echo=FALSE, results='asis'----------------------------- knitr::kable(entryDf, "pipe", caption="The entry returned when searching by description.") ## ----------------------------------------------------------------------------- mybiodb$terminate() ## ----------------------------------------------------------------------------- sessionInfo()