Skip to contents

Helper function for retrieving gtf files from ENSEMBL

Source: R/getENSEMBL.R
getENSEMBL.gtf.Rd

This function downloads gff files of query organisms from ENSEMBL.

Usage

getENSEMBL.gtf(organism, type = "dna", path, release = NULL)

Arguments

organism

Organism selector id, there are three options to characterize an organism:

  • by scientific name: e.g. organism = "Homo sapiens"

  • by database specific accession identifier: e.g. organism = "GCF_000001405.37" (= NCBI RefSeq identifier for Homo sapiens)

  • by taxonomic identifier from NCBI Taxonomy: e.g. organism = "9606" (= taxid of Homo sapiens)

type

character, biological sequence type (e.g. "dna", "cds")

path

location where file shall be stored.

release

a numeric, the database release version of ENSEMBL (db = "ensembl"). Default is release = NULL meaning that the most recent database version is used. release = 75 would for human would give the stable GRCh37 release in ensembl. Value must be > 46, since ensembl did not structure their data if the standard format before that.

Value

character filepath to download file, returns FALSE if failed.

Author

Hajk-Georg Drost