Helper function for retrieving gtf files from ENSEMBL — getENSEMBL.gtf • biomartr
Description: This function downloads gff files of query organisms from ENSEMBL.

# 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.

    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