## ----style, eval=TRUE, echo=FALSE, results='asis'-------------------------- BiocStyle::latex() ## ----include=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set(tidy=FALSE) ## ---- 0] # wantedp <- unique(unlist(wantedp)) # ans <- unlist(mget(wantedp, hgu95av2SYMBOL)) # }) # length(ans) # ans[1:10] ## ----schema, results='hide'------------------------------------------- hgu95av2_dbschema() ## ----schema2, results='hide'------------------------------------------ hgu95av2ORGPKG ## ----schema3, results='hide'------------------------------------------ org.Hs.eg_dbschema() ## ----hgu95av2_org_join, tidy=FALSE------------------------------------ orgDBLoc = system.file("extdata", "org.Hs.eg.sqlite", package="org.Hs.eg.db") attachSQL = paste("ATTACH '", orgDBLoc, "' AS orgDB;", sep = "") dbGetQuery(hgu95av2_dbconn(), attachSQL) ## ----complexDb-------------------------------------------------------- system.time({ SQL <- "SELECT DISTINCT probe_id,symbol FROM probes, orgDB.gene_info AS gi, orgDB.genes AS g, orgDB.go_bp AS bp WHERE bp._id=g._id AND gi._id=g._id AND probes.gene_id=g.gene_id AND bp.evidence IN ('IPI', 'IDA', 'IMP', 'IGI')" zz <- dbGetQuery(hgu95av2_dbconn(), SQL) }) #its a good idea to always DETACH your database when you are finished... dbGetQuery(hgu95av2_dbconn(), "DETACH orgDB" ) ## ----Question #6, echo=FALSE, results='hide'-------------------------- sql <- "SELECT gene_id, start_location, end_location, cytogenetic_location FROM genes AS g, chromosome_locations AS c, cytogenetic_locations AS cy WHERE g._id=c._id AND g._id=cy._id" dbGetQuery(org.Hs.eg_dbconn(),sql)[1:10,] ## ----Question #7, echo=FALSE, results='hide'-------------------------- orgDBLoc = system.file("extdata", "org.Hs.eg.sqlite", package="org.Hs.eg.db") attachSQL = paste("ATTACH '", orgDBLoc, "' AS orgDB;", sep = "") dbGetQuery(hgu95av2_dbconn(), attachSQL) goDBLoc = system.file("extdata", "GO.sqlite", package="GO.db") attachSQL = paste("ATTACH '", goDBLoc, "' AS goDB;", sep = "") dbGetQuery(hgu95av2_dbconn(), attachSQL) SQL <- "SELECT DISTINCT p.probe_id, gi.symbol, gt.go_id, gt.definition FROM probes AS p, orgDB.gene_info AS gi, orgDB.genes AS g, orgDB.go_bp AS bp, goDB.go_term AS gt WHERE bp._id=g._id AND gi._id=g._id AND p.gene_id=g.gene_id AND bp.evidence IN ('IPI', 'IDA', 'IMP', 'IGI') AND gt.go_id=bp.go_id" zz <- dbGetQuery(hgu95av2_dbconn(), SQL) dbGetQuery(hgu95av2_dbconn(), "DETACH orgDB") dbGetQuery(hgu95av2_dbconn(), "DETACH goDB") ## ----SessionInfo, echo=FALSE------------------------------------------ sessionInfo()