Skip to contents

This function downloads gff files of query organisms from ENSEMBL.

Usage

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

Arguments

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.

Value

character filepath to download file, returns FALSE if failed.

Author

Hajk-Georg Drost