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

Source: R/buildReferenceData.R

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

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)
#> Got local file: /private/var/folders/1t/jb58v7t17yz914q_spv5qt3w0000gn/T/RtmpHJib82/temp_libpath834f459db1b4/GenomicDistributions/extdata/C_elegans_cropped_example.gtf.gz