## ----dependencies, warning=FALSE, message=FALSE-------------------------- library(GenomicFeatures) library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## ----biocLite, eval=FALSE------------------------------------------------ ## source("http://www.bioconductor.org/biocLite.R") ## biocLite(c("GenomicFeatures", "TxDb.Hsapiens.UCSC.hg19.knownGene")) ## ----txdb---------------------------------------------------------------- library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene txdb ## ----gr------------------------------------------------------------------ gr <- GRanges(seqnames = "chr1", strand = "+", ranges = IRanges(start = 11874, end = 14409)) subsetByOverlaps(genes(txdb), gr) subsetByOverlaps(genes(txdb), gr, ignore.strand = TRUE) ## ----transcripts--------------------------------------------------------- subsetByOverlaps(transcripts(txdb), gr) ## ----exons--------------------------------------------------------------- subsetByOverlaps(exons(txdb), gr) ## ----exonsBy------------------------------------------------------------- subsetByOverlaps(exonsBy(txdb, by = "tx"), gr) ## ----cds----------------------------------------------------------------- subsetByOverlaps(cds(txdb), gr) subsetByOverlaps(cdsBy(txdb, by = "tx"), gr) ## ----transcriptLengths--------------------------------------------------- subset(transcriptLengths(txdb, with.cds_len = TRUE), gene_id == "100287102") ## ----sessionInfo, echo=FALSE--------------------------------------------- sessionInfo()