## ----------------------------------------------------------------------------- library(biobtreeR) # Create an folder and set as an output directory # It is used for database and configuration files # temporary directory is used for demonstration purpose bbUseOutDir(tempdir()) ## ----------------------------------------------------------------------------- # Called once and saves the built in database to local disk # Included datasets hgnc,hmdb,taxonomy,go,efo,eco,chebi,interpro # Included uniprot proteins and ensembl genomes belongs to following organisms: # homo_sapiens, danio_rerio(zebrafish), gallus_gallus(chicken), mus_musculus, Rattus norvegicus, saccharomyces_cerevisiae, # arabidopsis_thaliana, drosophila_melanogaster, caenorhabditis_elegans, Escherichia coli, Escherichia coli str. K-12 substr. MG1655, Escherichia coli K-12 # Requires ~ 6 GB free storage bbBuiltInDB() ## ----eval=FALSE--------------------------------------------------------------- # # # multiple species genomes supported with comma seperated taxonomy identifiers # bbBuildCustomDB(taxonomyIDs = "1408103,206403") # ## ----------------------------------------------------------------------------- bbStart() ## ----------------------------------------------------------------------------- bbSearch("tpi1,vav_human,ENST00000297261") ## ----------------------------------------------------------------------------- bbSearch("tpi1,ENSG00000164690","ensembl") ## ----------------------------------------------------------------------------- bbSearch("tpi1,vav_human,ENST00000297261",showURL =TRUE) ## ----------------------------------------------------------------------------- bbMapping("AT5G3_HUMAN",'map(go)',attrs = "type") ## ----------------------------------------------------------------------------- bbMapping("AT5G3_HUMAN",'map(go).filter(go.type=="biological_process")',attrs = "type") ## ----------------------------------------------------------------------------- bbListAttrs("go") ## ----------------------------------------------------------------------------- bbListAttrs("uniprot") ## ----------------------------------------------------------------------------- bbListAttrs("hgnc") ## ----------------------------------------------------------------------------- bbListAttrs("ensembl") ## ----------------------------------------------------------------------------- bbListAttrs("transcript") ## ----------------------------------------------------------------------------- bbListAttrs("exon") ## ----------------------------------------------------------------------------- bbListAttrs("cds") ## ----------------------------------------------------------------------------- res<-bbMapping("ATP5MC3,TP53",'map(transcript)') head(res) ## ----------------------------------------------------------------------------- res<-bbMapping("ATP5MC3,TP53",'map(transcript).map(exon)',attrs = "seq_region") head(res) ## ----------------------------------------------------------------------------- res<-bbMapping("shh",'filter(ensembl.genome=="homo_sapiens").map(ortholog)') head(res) ## ----------------------------------------------------------------------------- bbMapping("fry,mog",'map(paralog)',showInputColumn = TRUE) ## ----------------------------------------------------------------------------- bbMapping("ENSG00000073910,shh" ,'map(entrez)') ## ----------------------------------------------------------------------------- bbMapping("NM_005359,NM_000546",'map(hgnc)',attrs = "symbols") ## ----------------------------------------------------------------------------- res<-bbMapping("homo_sapiens",'map(ensembl).filter(ensembl.seq_region=="Y" && ensembl.biotype=="lncRNA")',attrs = 'name') head(res) ## ----------------------------------------------------------------------------- bbMapping("tpi1,shh",'map(transcript).map(cds)') ## ----------------------------------------------------------------------------- bbMapping("9606",'map(ensembl).filter((114129278>ensembl.start && 114129278ensembl.start && 114129328 45000)" ,attrs = "sequence$mass,sequence$seq") ## ----------------------------------------------------------------------------- bbMapping("shh_human",'map(ufeature).filter(ufeature.type=="helix")' ,attrs = "location$begin,location$end") ## ----------------------------------------------------------------------------- bbMapping("tp53",'map(uniprot).map(ufeature).filter(ufeature.original=="I" && ufeature.variation=="S").map(variantid)',source = "hgnc") ## ----------------------------------------------------------------------------- bbStop() ## ----------------------------------------------------------------------------- sessionInfo()