getENSEMBL.gtf: Helper function for retrieving gtf files from ENSEMBL

In HajkD/biomartr: Genomic Data Retrieval

Helper function for retrieving gtf files from ENSEMBL

Description

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(s)

Hajk-Georg Drost

HajkD/biomartr documentation built on Dec. 9, 2023, 7:25 p.m.