read_assemblystats

a character string specifying the path to the file storing 
the Genome Assembly Stats file.

file

either <code>type = "raw"</code> to import the entire genome assembly 
stats file or <code>type = "stats"</code> to import overall statistics including 
all chromosomes, mitochondria and plastids.

type

This function reads an organism specific Genome Assembly 
Stats file that was retrieved with <code><a rd-options="" href="/link/getAssemblyStats?package=biomartr&version=0.9.0" data-mini-rdoc="biomartr::getAssemblyStats">getAssemblyStats</a></code>.

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_assemblystats function

This function reads an organism specific Genome Assembly 
Stats file that was retrieved with <code><a rd-options='' href='getAssemblyStats'>getAssemblyStats</a></code>.

read_assemblystats: Import Genome Assembly Stats File

Description

Usage

Arguments

Details

See Also