getGeneModelsFromGTF {GenomicDistributions}R Documentation

Get gene models from a remote or local GTF file

Description

Get gene models from a remote or local GTF file

Usage

getGeneModelsFromGTF(
  source,
  features,
  convertEnsemblUCSC = FALSE,
  destDir = NULL
)

Arguments

source

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

features

a vector of strings with feature identifiers that to include in the result list

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"
features = c("gene", "exon", "three_prime_utr", "five_prime_utr")
CElegansGeneModels = getGeneModelsFromGTF(CElegansGtfUrl, features, TRUE)

[Package GenomicDistributions version 1.2.0 Index]