## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install('biodbNcbi') ## ----results='hide'----------------------------------------------------------- mybiodb <- biodb::newInst() ## ----------------------------------------------------------------------------- gene <- mybiodb$getFactory()$createConn('ncbi.gene') ## ----------------------------------------------------------------------------- ccds <- mybiodb$getFactory()$createConn('ncbi.ccds') pubchem.comp <- mybiodb$getFactory()$createConn('ncbi.pubchem.comp') pubchem.subst <- mybiodb$getFactory()$createConn('ncbi.pubchem.subst') ## ----------------------------------------------------------------------------- gene$getNbEntries() ## ----------------------------------------------------------------------------- ids <- gene$getEntryIds(2) ids ## ----------------------------------------------------------------------------- entries <- gene$getEntry(ids) entries ## ----------------------------------------------------------------------------- x <- mybiodb$entriesToDataframe(entries) x ## ----------------------------------------------------------------------------- entryxml <- gene$wsEfetch('2833', retmode='xml', retfmt='parsed') XML::getNodeSet(entryxml, "//Entrezgene_prot") ## ----------------------------------------------------------------------------- gene$wsEsearch(term='"chemokine"[Gene Name]', retmax=10, retfmt='ids') ## ----------------------------------------------------------------------------- gene$searchForEntries(fields=list(name='chemokine'), max.results=10) ## ----------------------------------------------------------------------------- infoxml <- pubchem.comp$wsEinfo(retfmt='parsed') XML::getNodeSet(infoxml, "//Field[1]") ## ----------------------------------------------------------------------------- mybiodb$terminate() ## ----------------------------------------------------------------------------- sessionInfo()