getENSEMBL

Backend function for retrieving files sequence and annotation
files from the ENSEMBL ftp server

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized
way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',
and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database
(Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve
functional annotation for genomic loci. In addition, users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.

Hajk-Georg Drost

biomartr

Genomic Data Retrieval

Haakon Tjeldnes

getENSEMBL function

<dl><dt>organism</dt>
<dd>Organism selector id,
there are three options to characterize an organism:<ul>
<li>by <code>scientific name</code>: e.g. <code>organism = "Homo sapiens"</code></li>
<li>by <code>database specific accession identifier</code>: e.g. <code>organism = "GCF_000001405.37"</code> (= NCBI RefSeq identifier for <code>Homo sapiens</code>)</li>
<li>by <code>taxonomic identifier from NCBI Taxonomy</code>: e.g. <code>organism = "9606"</code> (= taxid of <code>Homo sapiens</code>)</li>
</ul></dd>
<dt>type</dt>
<dd>character, biological sequence type (e.g. "dna", "cds")</dd>
<dt>id.type</dt>
<dd>a character, default "toplevel".
id type of assembly, either "toplevel" or "primary_assembly" for genomes.
Can be other strings, for non genome objects.</dd>
<dt>release</dt>
<dd>a numeric, the database release version of ENSEMBL (<code>db = "ensembl"</code>). Default is <code>release = NULL</code> meaning
that the most recent database version is used. <code>release = 75</code> would for human would give the stable
GRCh37 release in ensembl. Value must be &gt; 46, since ensembl did not structure their data
if the standard format before that.</dd>
<dt>path</dt>
<dd>location where file shall be stored.</dd>
<dt>format</dt>
<dd>"gff3", alternative "gtf" for ensembl.</dd></dl>

Arguments

Author

Download sequence or annotation from ENSEMBL — getENSEMBL

<dl>

<dt>organism</dt>
<dd>Organism selector id,
there are three options to characterize an organism:<ul>
<li>by <code>scientific name</code>: e.g. <code>organism = "Homo sapiens"</code></li>
<li>by <code>database specific accession identifier</code>: e.g. <code>organism = "GCF_000001405.37"</code> (= NCBI RefSeq identifier for <code>Homo sapiens</code>)</li>
<li>by <code>taxonomic identifier from NCBI Taxonomy</code>: e.g. <code>organism = "9606"</code> (= taxid of <code>Homo sapiens</code>)</li>
</ul></dd>


<dt>type</dt>
<dd>character, biological sequence type (e.g. "dna", "cds")</dd>


<dt>id.type</dt>
<dd>a character, default "toplevel".
id type of assembly, either "toplevel" or "primary_assembly" for genomes.
Can be other strings, for non genome objects.</dd>


<dt>release</dt>
<dd>a numeric, the database release version of ENSEMBL (<code>db = "ensembl"</code>). Default is <code>release = NULL</code> meaning
that the most recent database version is used. <code>release = 75</code> would for human would give the stable
GRCh37 release in ensembl. Value must be &gt; 46, since ensembl did not structure their data
if the standard format before that.</dd>


<dt>path</dt>
<dd>location where file shall be stored.</dd>


<dt>format</dt>
<dd>"gff3", alternative "gtf" for ensembl.</dd>

</dl>

getENSEMBL: Download sequence or annotation from ENSEMBL

Description

Usage

Value

Arguments

Author