getENSEMBL.gtf

scientific name of the organism of interest.

organism

type

a character, default "toplevel". id type of assembly, either toplevel or primary_assembly usually.

id.type

location where file shall be stored.

path

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.

release

This function downloads gff
files of query organisms from ENSEMBL.

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

getENSEMBL.gtf function

<dl><dt>organism</dt>
<dd>scientific name of the organism of interest.</dd>
<dt>type</dt>
<dd>biological sequence type.</dd>
<dt>id.type</dt>
<dd>a character, default "toplevel". id type of assembly, either toplevel or primary_assembly usually.</dd>
<dt>path</dt>
<dd>location where file shall be stored.</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></dl>

Arguments

Author

Helper function for retrieving gff files from ENSEMBL — getENSEMBL.gtf

<dl>

<dt>organism</dt>
<dd>scientific name of the organism of interest.</dd>


<dt>type</dt>
<dd>biological sequence type.</dd>


<dt>id.type</dt>
<dd>a character, default "toplevel". id type of assembly, either toplevel or primary_assembly usually.</dd>


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

</dl>

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

Description

Usage

Value

Arguments

Author