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Download GTF File from the GENCODE Database

Source: R/files.R
get_gtf.Rd

Downloads a GTF file for a specified species, release version, and annotation type from the GENCODE database. The file is saved to a user-specified directory or the current working directory by default.

Usage

get_gtf(species, release_version, annotation_type, dest_folder)

Arguments

species

A character string indicating the species. Supported values are:

  • "human"

  • "mouse"

release_version

A character string specifying the release version. Options include:

  • "latest_release": Automatically fetches the latest release for the specified species.

  • "release_X": Specific human release (e.g., "release_47").

  • "release_MX": Specific mouse release (e.g., "release_M36").

annotation_type

A character string specifying the annotation type. Valid options are:

  • "annotation.gtf.gz"

  • "basic.annotation.gtf.gz"

  • "chr_patch_hapl_scaff.annotation.gtf.gz"

  • "chr_patch_hapl_scaff.basic.annotation.gtf.gz"

  • "long_noncoding_RNAs.gtf.gz"

  • "primary_assembly.annotation.gtf.gz"

  • "primary_assembly.basic.annotation.gtf.gz"

  • "tRNAs.gtf.gz"

  • "polyAs.gtf.gz"

dest_folder

A character string specifying the destination folder where the file will be downloaded. Defaults to the current working directory.

Value

A character string specifying the path to the downloaded GTF file.

Details

The function dynamically determines the correct file URL based on the provided parameters and downloads the GTF file to the desired location. If "latest_release" is specified for release_version, the function will first determine the latest available release using get_latest_release().

Examples

# \donttest{
# Download the latest human GTF file with primary assembly annotations into a temp directory
temp_dir <- tempdir()
gtf_file <- get_gtf(
  species = "human",
  release_version = "latest_release",
  annotation_type = "primary_assembly.basic.annotation.gtf.gz",
  dest_folder = temp_dir
)
#> Latest human GENCODE release: release_48
#> Downloading GTF file from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.primary_assembly.basic.annotation.gtf.gz
#> GTF file downloaded successfully: /tmp/Rtmpt3phjF/gencode.v48.primary_assembly.basic.annotation.gtf.gz
print(gtf_file)
#> [1] "/tmp/Rtmpt3phjF/gencode.v48.primary_assembly.basic.annotation.gtf.gz"

# Download a specific mouse release with long noncoding RNA annotations into a temp directory
temp_dir <- tempdir()
gtf_file <- get_gtf(
  species = "mouse",
  release_version = "release_M36",
  annotation_type = "long_noncoding_RNAs.gtf.gz",
  dest_folder = temp_dir
)
#> Downloading GTF file from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M36/gencode.vM36.long_noncoding_RNAs.gtf.gz
#> GTF file downloaded successfully: /tmp/Rtmpt3phjF/gencode.vM36.long_noncoding_RNAs.gtf.gz
print(gtf_file)
#> [1] "/tmp/Rtmpt3phjF/gencode.vM36.long_noncoding_RNAs.gtf.gz"
# }