read_assemblystats

This function reads an organism specific Genome Assembly
Stats file that was retrieved with <code>getAssemblyStats</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',
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. with only one command.

Hajk-Georg Drost

biomartr

Genomic Data Retrieval

Haakon Tjeldnes

read_assemblystats function

<dl><dt>file</dt>
<dd>a character string specifying the path to the file storing
the Genome Assembly Stats file.</dd>
<dt>type</dt>
<dd>a tibble object, 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.</dd></dl>

Arguments

Author

Import Genome Assembly Stats File — read_assemblystats

<dl>

<dt>file</dt>
<dd>a character string specifying the path to the file storing
the Genome Assembly Stats file.</dd>


<dt>type</dt>
<dd>a tibble object, 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.</dd>

</dl>

read_assemblystats: Import Genome Assembly Stats File

Description

Usage

Arguments

Author

Details

See Also