# #——风格,eval = TRUE,呼应= FALSE,结果=“黑名单”- - - - - - - - - - - - - - - - - - - - - - - - - - - - BiocStyle::乳胶()# #——包括= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(knitr)美元opts_chunk组(整洁= FALSE) # # - - - - - 0]# wantedp < -独特(unlist (wantedp)) # ans <——unlist (mget (wantedp hgu95av2SYMBOL)) #}) #长度(ans) # ans[1:10] # #——模式,结果=“隐藏”- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hgu95av2_dbschema () # #——schema2,结果=“隐藏”- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - hgu95av2ORGPKG # #——schema3,结果=“隐藏”- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - org.Hs.eg_dbschema () # #——hgu95av2_org_join,整洁= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - orgDBLoc =系统。文件(“extdata”、“org.Hs.eg。sqlite”,包= " org.Hs.eg.db”) attachSQL =粘贴(“附加”“orgDBLoc,”“orgDB;”,9 = " ")dbGetQuery (hgu95av2_dbconn (), attachSQL) # #——complexDb - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -系统。时间({SQL <——“从探针选择不同probe_id,象征,orgDB。gene_info gi, orgDB。基因g, orgDB。go_bp bp bp._id = g。_id gi._id = g。_id probes.gene_id = g。gene_id和英国石油公司。证据(“他们”,“艾达”,“小淘气”,“IGI”)“zz < - dbGetQuery (hgu95av2_dbconn (), SQL)}) #一个好主意总是分离数据库当你完成的时候…dbGetQuery (hgu95av2_dbconn(),“分离orgDB”) # # # 6 - - - - -问题,呼应= FALSE,结果=“隐藏”- - - - - - - - - - - - - - - - - - - - - - - - - - - - sql <——“选择gene_id、start_location end_location, cytogenetic_location从基因g, chromosome_locations c, cytogenetic_locations cy g._id = c。_id和g._id = cy。_id“dbGetQuery (org.Hs.eg_dbconn (), sql)[1:10], # # # 7 - - - - -问题,呼应= FALSE,结果=“隐藏”- - - - - - - - - - - - - - - - - - - - - - - - - - - - orgDBLoc =系统。文件(“extdata”、“org.Hs.eg。sqlite”,包= " org.Hs.eg.db”) attachSQL =粘贴(“附加”“orgDBLoc,”“orgDB;”,9 = " ")dbGetQuery (hgu95av2_dbconn (), attachSQL) goDBLoc =系统。文件(“extdata”、“走。sqlite”,包= " GO.db”) attachSQL =粘贴(“附加”“goDBLoc,”“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()