read_proteome

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

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
<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>.

This function reads an organism specific proteome 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_proteome function

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

read_proteome: Import Proteome as Biostrings or data.table object

Description

Usage

Arguments

Value

Details

See Also