# #——loadGenomicFeatures ------------------------------------------------------ (“GenomicFeatures suppressPackageStartupMessages(图书馆 ')) ## ---- loadDb ------------------------------------------------------------------- samplefile < -系统。文件(“extdata”、“hg19_knownGene_sample。sqlite”,包= " GenomicFeatures”)txdb < - loadDb (samplefile) txdb # #——loadPackage -------------------------------------------------------------- 库(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb < - TxDb.Hsapiens.UCSC.hg19。knownGene #速记(为了方便)txdb # #——seqlevels ---------------------------------------------------------------- 头(seqlevels (txdb )) ## ---- seqlevels2 --------------------------------------------------------------- seqlevels (txdb) <——“chr1”# #——seqlevels3 --------------------------------------------------------------- seqlevels (txdb) < - seqlevels0 (txdb) # #——seqlevels4 --------------------------------------------------------------- seqlevels (txdb) <——“chr15”seqlevels (txdb) # #——selectExample ------------------------------------------------------------ 键< - c(“100033416”、“100033417”、“100033420”)列(txdb) keytypes (txdb)选择(txdb键=键列=“TXNAME keytype = " GENEID ") ## ---- selectExercise ----------------------------------------------------------- 列(txdb)关口< - c(“TXNAME”、“TXSTRAND”、“TXCHROM”)选择(txdb键=键列=关口,keytype = " GENEID ") ## ---- transcripts1 ------------------------------------------------------------- GR < -成绩单(txdb) GR[1:3] # #——transcripts2 ------------------------------------------------------------- tx_strand < -链(GR) tx_strand总和(runLength (tx_strand)) (GR) # #——transcripts3长度 ------------------------------------------------------------- GR < -成绩单(txdb、过滤=列表(tx_chrom =“chr15”,tx_strand = " + "))长度(链(GR (GR)独一无二的 )) ## ---- transcripts4 ------------------------------------------------------------- 公关< -促进剂(txdb上游= 2000,下游= 400)公关# #——exonsExer1 --------------------------------------------------------------- < -交货外显子(txdb)[1:4]交货长度(特异)(GR) # #——transcriptsBy ------------------------------------------------------------ GRList < - transcriptsBy (txdb=“基因”)长度(GRList)名称(GRList) [13] GRList[数]# #——exonsBy ------------------------------------------------------------------ GRList < - exonsBy (txdb = tx)长度(GRList)名称(GRList) [13] GRList [[12 ]] ## ---- internalID --------------------------------------------------------------- GRList < - exonsBy (txdb = tx) tx_ids < -名字(GRList)头(select (txdb键= tx_ids列=“TXNAME”,keytype = " TXID ")) ## ---- introns-UTRs ------------------------------------------------------------- 长度(intronsByTranscript (txdb))长度(fiveUTRsByTranscript (txdb)) (threeUTRsByTranscript (txdb长度 )) ## ---- 提取 ------------------------------------------------------------------ 库(BSgenome.Hsapiens.UCSC.hg19) tx_seqs1 < extractTranscriptSeqs (Hsapiens TxDb.Hsapiens.UCSC.hg19。knownGene use.names = TRUE) # #——translate1 --------------------------------------------------------------- suppressWarnings(翻译(tx_seqs1 )) ## ---- betterTranslation -------------------------------------------------------- cds_seqs < - extractTranscriptSeqs (Hsapiens cdsBy (txdb, =“tx”,use.names = TRUE))翻译(cds_seqs) # #——supportedUCSCtables ------------------------------------------------------ supportedUCSCtables(基因组= " mm9 ") ## ---- makeTxDbFromUCSC,eval = FALSE --------------------------------------------- # mm9KG_txdb < - makeTxDbFromUCSC(基因组=“mm9”,表= " knownGene ") ## ---- makeTxDbFromBiomart eval = FALSE ------------------------------------------ # mmusculusEnsembl < makeTxDbFromBiomart(数据集= " mmusculus_gene_ensembl ") ## ---- saveDb-1 eval = FALSE ----------------------------------------------------- # =“fileName.sqlite saveDb (mm9KG_txdb文件 ") ## ---- loadDb-1, eval=FALSE----------------------------------------------------- # mm9KG_txdb <- loadDb("fileName.sqlite") ## ----SessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()