getTssFromGTF {GenomicDistributions}R Documentation

Get transcription start sites (TSSs) from a remote or local GTF file

Description

Get transcription start sites (TSSs) from a remote or local GTF file

Usage

getTssFromGTF(source, convertEnsemblUCSC = FALSE, destDir = NULL)

Arguments

source

a string that is either a path to a local or remote GTF

convertEnsemblUCSC

a logical indicating whether Ensembl style chromosome annotation should be changed to UCSC style

destDir

a string that indicates the path to the directory where the downloaded GTF file should be stored

Value

a list of GRanges objects

Examples

CElegansGtfUrl = "http://ftp.ensembl.org/pub/release-103/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.103.gtf.gz"
CElegansTss = getTssFromGTF(CElegansGtfUrl, TRUE)

[Package GenomicDistributions version 1.2.0 Index]