Helper function for retrieving gff files from ENSEMBL

This function downloads gff files of query organisms from ENSEMBL.

Usage

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

organism: scientific name of the organism of interest.
type: biological sequence type.
id.type: a character, default "toplevel". id type of assembly, either toplevel or primary_assembly usually.
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.

character filepath to download file, returns FALSE if failed.

Hajk-Georg Drost