read_genome

a character string specifying the path to the file 
storing the genome.

file

a character string specifying the file format used to store 
the genome, e.g. <code>format = &quot;fasta&quot;</code> (default) or <code>format = &quot;gbk&quot;</code>.

format

a character string specifying the object stype in which 
the genomic sequence shall be represented. Either as 
<code>obj.type = &quot;Biostrings&quot;</code> (default) or 
as <code>obj.type = &quot;data.table&quot;</code>.

obj.type

additional arguments that are used by the 
<code><a rd-options="seqinr" href="/link/read.fasta?package=biomartr&version=0.5.1&to=seqinr" data-mini-rdoc="seqinr::read.fasta">read.fasta</a></code> function.

This function reads an organism specific genome stored in a 
defined file format.

Perform metagenomic data retrieval and functional annotation
retrieval. In detail, this package aims to provide users with a standardized
way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI' and 'ENSEMBL' 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. Users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as
well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

Hajk-Georg Drost

biomartr

Genomic Data Retrieval

read_genome function

additional arguments that are used by the 
<code><a rd-options='seqinr' href='read.fasta'>read.fasta</a></code> function.

read_genome: Import Genome Assembly as Biostrings or data.table object

Description

Usage

Arguments

Value

Details

See Also