## ----style, eval=TRUE, echo=FALSE，结果= ' asis '-------------------------- BiocStyle:乳胶 () ## ---- 包括= FALSE --------------------------------------------------------- 图书馆(knitr)美元opts_chunk组(整洁= FALSE) # #——loadChip -------------------------------------------------------------- suppressPackageStartupMessages({库(hgu95av2.db ) }) ## ---- listContents ---------------------------------------------------------- ls(“包:hgu95av2.db ") ## ---- 显示 ------------------------------------------------------------------hgu95av2.db # #——列 --------------------------------------------------------------- 列(hgu95av2.db) # #——帮助,eval = FALSE ------------------------------------------------------ # 帮助(“象征 ") ## ---- keytypes -------------------------------------------------------------- keytypes (hgu95av2.db) # #——钥匙 ------------------------------------------------------------------ (钥匙(hgu95av2.dbkeytype = "符号 ")) ## ---- selectChip ------------------------------------------------------------ # 1日得到一些示例键k < -头(键(hgu95av2.db, keytype =“PROBEID”))#然后调用选择选择(hgu95av2.db键= k,列= c(“象征”、“GENENAME”),keytype = " PROBEID ") ## ---- mapIdsChip ------------------------------------------------------------ # 1日得到一些示例键k < -头(键(hgu95av2.db, keytype =“PROBEID”))#然后调用mapIds mapIds (hgu95av2.db键= k,列= c(“GENENAME”),keytype = " PROBEID ") ## ---- selectOrg1 ------------------------------------------------------------ 库(org.Hs.eg.db)列(org.Hs.eg.db) # #——selectOrg2 eval = FALSE ------------------------------------------------ # 帮助(“象征”)# #的解释这些列和# #——selectOrg3 keytypes值 ------------------------------------------------------------ keytypes (org.Hs.eg.db) uniKeys < -头(键(org.Hs.eg.db, keytype =“UNIPROT”))关口< - c(“象征”、“路径”)选择(org.Hs.eg.db,键= uniKeys列=关口,keytype = " UNIPROT ") ## ---- selectData ------------------------------------------------------------ 负载(系统。文件(“extdata”、“resultTable。Rda”,包= " AnnotationDbi "))头(resultTable) # #——selectOrgData --------------------------------------------------------- annots < - select (org.Hs.eg.db键= rownames (resultTable),列= c(“象征”、“GENENAME”),keytype =“ENTREZID”)resultTable < - (resultTable, annots合并。x = 0, by.y =“ENTREZID”)负责人(resultTable) # #——selectGO -------------------------------------------------------------- 库(GO.db) GOIDs < - c(“去:0042254”,“去:0044183”)选择(GO.db键= GOIDs列=“定义”,keytype = " GOID ") ## ---- selectTxDb ------------------------------------------------------------ 库(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb < - TxDb.Hsapiens.UCSC.hg19。knownGene txdb列(txdb) keytypes (txdb)键< -头(键(txdb, keytype =“GENEID”))关口< - c(“TXID”、“TXSTART”)选择(txdb键=键列=关口,keytype = " GENEID ") ## ---- selectEnsDb ----------------------------------------------------------- 库(EnsDb.Hsapiens.v75)教育局< - EnsDb.Hsapiens。v75 edb# #列出所有列列(edb) ##列出所有键类型键类型(edb) ##获取第一个键<-头(键(edb, keytype="GENEID")) ##获取数据select(edb, keys=keys, columns=c("TXID"， "TXSEQSTART"， "TXBIOTYPE")， keytype="GENEID") ## ----selectEnsDb。Y --------------------------------------------------------- ## 检索所有基因的id lincRNAs Y染色体上编码linkY < -键(教育局、过滤=列表(GeneBiotypeFilter(“lincRNA”),SeqNameFilter (" Y ")))长度(linkY) # #我们现在所有这些基因的转录。txs <- select(edb, keys=linkY, columns=c("TXID"， "TXSEQSTART"， "TXBIOTYPE")， keytype="GENEID") nrow(txs) ##或者，我们可以用keys参数指定/传递过滤器。 txs <- select(edb, keys=list(GeneBiotypeFilter("lincRNA"), SeqNameFilter("Y")), columns=c("TXID", "TXSEQSTART", "TXBIOTYPE")) nrow(txs) ## ----SessionInfo, echo=FALSE----------------------------------------------- sessionInfo()