## ----style, eval=TRUE, echo=FALSE, results='asis'-------------------------- BiocStyle::latex() ## ----loadGenomicFeatures--------------------------------------------------- suppressPackageStartupMessages(library('GenomicFeatures')) ## ----loadDb---------------------------------------------------------------- samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite", package="GenomicFeatures") txdb <- loadDb(samplefile) txdb ## ----loadPackage----------------------------------------------------------- library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene #shorthand (for convenience) txdb ## ----seqlevels------------------------------------------------------------- head(seqlevels(txdb)) ## ----seqlevels2------------------------------------------------------------ seqlevels(txdb) <- "chr1" ## ----seqlevels3------------------------------------------------------------ seqlevels(txdb) <- seqlevels0(txdb) ## ----seqlevels4------------------------------------------------------------ seqlevels(txdb) <- "chr15" seqlevels(txdb) ## ----selectExample--------------------------------------------------------- keys <- c("100033416", "100033417", "100033420") columns(txdb) keytypes(txdb) select(txdb, keys = keys, columns="TXNAME", keytype="GENEID") ## ----selectExercise-------------------------------------------------------- columns(txdb) cols <- c("TXNAME", "TXSTRAND", "TXCHROM") select(txdb, keys=keys, columns=cols, keytype="GENEID") ## ----transcripts1---------------------------------------------------------- GR <- transcripts(txdb) GR[1:3] ## ----transcripts2---------------------------------------------------------- tx_strand <- strand(GR) tx_strand sum(runLength(tx_strand)) length(GR) ## ----transcripts3---------------------------------------------------------- GR <- transcripts(txdb, filter=list(tx_chrom = "chr15", tx_strand = "+")) length(GR) unique(strand(GR)) ## ----transcripts4---------------------------------------------------------- PR <- promoters(txdb, upstream=2000, downstream=400) PR ## ----exonsExer1------------------------------------------------------------ EX <- exons(txdb) EX[1:4] length(EX) length(GR) ## ----transcriptsBy--------------------------------------------------------- GRList <- transcriptsBy(txdb, by = "gene") length(GRList) names(GRList)[10:13] GRList[11:12] ## ----exonsBy--------------------------------------------------------------- GRList <- exonsBy(txdb, by = "tx") length(GRList) names(GRList)[10:13] GRList[[12]] ## ----internalID------------------------------------------------------------ GRList <- exonsBy(txdb, by = "tx") tx_ids <- names(GRList) head(select(txdb, keys=tx_ids, columns="TXNAME", keytype="TXID")) ## ----introns-UTRs---------------------------------------------------------- length(intronsByTranscript(txdb)) length(fiveUTRsByTranscript(txdb)) length(threeUTRsByTranscript(txdb)) ## ----extract--------------------------------------------------------------- library(BSgenome.Hsapiens.UCSC.hg19) tx_seqs1 <- extractTranscriptSeqs(Hsapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, use.names=TRUE) ## ----translate1------------------------------------------------------------ suppressWarnings(translate(tx_seqs1)) ## ----betterTranslation----------------------------------------------------- cds_seqs <- extractTranscriptSeqs(Hsapiens, cdsBy(txdb, by="tx", use.names=TRUE)) translate(cds_seqs) ## ----supportedUCSCtables--------------------------------------------------- supportedUCSCtables(genome="mm9") ## ----makeTxDbFromUCSC, eval=FALSE------------------------------------------ # mm9KG_txdb <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene") ## ----makeTxDbFromBiomart, eval=FALSE--------------------------------------- # mmusculusEnsembl <- makeTxDbFromBiomart(dataset="mmusculus_gene_ensembl") ## ----saveDb-1, eval=FALSE-------------------------------------------------- # saveDb(mm9KG_txdb, file="fileName.sqlite") ## ----loadDb-1, eval=FALSE-------------------------------------------------- # mm9KG_txdb <- loadDb("fileName.sqlite") ## ----SessionInfo, echo=FALSE----------------------------------------------- sessionInfo()