getTssFromGTF: Get transcription start sites (TSSs) from a remote or local...

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

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,
  filterProteinCoding = TRUE
)

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
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")
CElegansTss = getTssFromGTF(CElegansGtfCropped, TRUE)

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