R/getENSEMBL.R
getENSEMBL.Seq.RdThis function downloads gff files of query organisms from ENSEMBL.
getENSEMBL.Seq(
organism,
type = "dna",
id.type = "toplevel",
release = NULL,
path
)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)
character, biological sequence type (e.g. "dna", "cds")
a character, default "toplevel". id type of assembly, either "toplevel" or "primary_assembly" for genomes. Can be other strings, for non genome objects.
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.
location where file shall be stored.
either a character path to downloaded file, or a logical FALSE, specifying failure.