## ----installgenomicfeatures, eval=FALSE--------------------------------------- # if (!require("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # # BiocManager::install("GenomicFeatures") ## ----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) hg19_txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene # shorthand (for convenience) hg19_txdb ## ----seqlevels---------------------------------------------------------------- head(seqlevels(hg19_txdb)) ## ----seqlevels2--------------------------------------------------------------- seqlevels(hg19_txdb) <- "chr1" ## ----seqlevels3--------------------------------------------------------------- seqlevels(hg19_txdb) <- seqlevels0(hg19_txdb) ## ----seqlevels4--------------------------------------------------------------- seqlevels(hg19_txdb) <- "chr15" seqlevels(hg19_txdb) ## ----selectExample------------------------------------------------------------ keys <- c("100033416", "100033417", "100033420") columns(hg19_txdb) keytypes(hg19_txdb) select(hg19_txdb, keys = keys, columns="TXNAME", keytype="GENEID") ## ----selectExercise----------------------------------------------------------- columns(hg19_txdb) cols <- c("TXNAME", "TXSTRAND", "TXCHROM") select(hg19_txdb, keys=keys, columns=cols, keytype="GENEID") ## ----transcripts1------------------------------------------------------------- GR <- transcripts(hg19_txdb) GR[1:3] ## ----transcripts2------------------------------------------------------------- tx_strand <- strand(GR) tx_strand sum(runLength(tx_strand)) length(GR) ## ----transcripts3------------------------------------------------------------- GR <- transcripts(hg19_txdb, filter=list(tx_chrom = "chr15", tx_strand = "+")) length(GR) unique(strand(GR)) ## ----transcripts4------------------------------------------------------------- PR <- promoters(hg19_txdb, upstream=2000, downstream=400) PR ## ----exonsExer1--------------------------------------------------------------- EX <- exons(hg19_txdb) EX[1:4] length(EX) length(GR) ## ----transcriptsBy------------------------------------------------------------ GRList <- transcriptsBy(hg19_txdb, by = "gene") length(GRList) names(GRList)[10:13] GRList[11:12] ## ----exonsBy------------------------------------------------------------------ GRList <- exonsBy(hg19_txdb, by = "tx") length(GRList) names(GRList)[10:13] GRList[[12]] ## ----internalID--------------------------------------------------------------- GRList <- exonsBy(hg19_txdb, by = "tx") tx_ids <- names(GRList) head(select(hg19_txdb, keys=tx_ids, columns="TXNAME", keytype="TXID")) ## ----introns-UTRs------------------------------------------------------------- length(intronsByTranscript(hg19_txdb)) length(fiveUTRsByTranscript(hg19_txdb)) length(threeUTRsByTranscript(hg19_txdb)) ## ----extract------------------------------------------------------------------ suppressPackageStartupMessages(library(BSgenome.Hsapiens.UCSC.hg19)) genome <- BSgenome.Hsapiens.UCSC.hg19 # shorthand (for convenience) tx_seqs1 <- extractTranscriptSeqs(genome, hg19_txdb, use.names=TRUE) ## ----translate1--------------------------------------------------------------- suppressWarnings(translate(tx_seqs1)) ## ----betterTranslation-------------------------------------------------------- cds_seqs <- extractTranscriptSeqs(Hsapiens, cdsBy(hg19_txdb, by="tx", use.names=TRUE)) translate(cds_seqs) ## ----SessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()