read_assemblystats

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

file

either <code>type = &quot;raw&quot;</code> to import the entire genome assembly 
stats file or <code>type = &quot;stats&quot;</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=0.5.1" data-mini-rdoc="biomartr::getAssemblyStats">getAssemblyStats</a></code>.

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_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