## ----setup, echo=FALSE--------------------------------------------------- suppressPackageStartupMessages({ library(UseBioconductor) library(GenomicRanges) }) stopifnot(BiocInstaller::biocVersion() == "3.1") ## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() knitr::opts_chunk$set(tidy=FALSE) ## ------------------------------------------------------------------------ library(GenomicRanges) showClass("GRangesList") ## ------------------------------------------------------------------------ library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene tx_by_gn <- transcriptsBy(txdb, by="gene") unlisted <- unlist(tx_by_gn) TSS <- ifelse(strand(unlisted) == "+", start(unlisted), end(unlisted)) TSS <- GRanges(seqnames(unlisted), IRanges(TSS, width=1), strand(unlisted)) TSS_by_gn <- relist(TSS, tx_by_gn) mcols(TSS) <- mcols(unlisted) TSS_by_gn <- relist(TSS, tx_by_gn)