getGeneModelsFromGTF: Get gene models from a remote or local GTF file

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

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,
  filterProteinCoding = TRUE
)

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
filterProteinCoding	a logical indicating if TSSs should be only protein-coding genes (default = TRUE)

Value

a list of GRanges objects

Examples

CElegansGtfCropped = system.file("extdata", 
                                 "C_elegans_cropped_example.gtf.gz", 
                                 package="GenomicDistributions")
features = c("gene", "exon", "three_prime_utr", "five_prime_utr")
CElegansGeneModels = getGeneModelsFromGTF(CElegansGtfCropped, features, TRUE)

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.