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 = "fasta"</code> (default) or <code>format = "gbk"</code>.

format

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

obj.type

additional arguments that are used by the 
<code><a rd-options="seqinr" href="/link/read.fasta?package=biomartr&version=0.9.0&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 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', 'ENSEMBLGENOMES',
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. 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