getAccessions

Find accessions numbers for a given taxa ID the NCBI taxonomy. This will be pretty slow unless the database was built with indexTaxa=TRUE since the database would not have an index for taxaId.

Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.

Scott Sherrill-Mix

taxonomizr

Functions to Work with NCBI Accessions and Taxonomy

getAccessions function

<dl><dt>taxaId</dt>
<dd>a vector of taxonomic IDs</dd>
<dt>sqlFile</dt>
<dd>a string giving the path to a SQLite file created by <code>read.accession2taxid</code></dd>
<dt>version</dt>
<dd>either 'version' indicating that taxaids are versioned e.g. Z17427.1 or 'base' indicating that taxaids do not have version numbers e.g. Z17427</dd>
<dt>limit</dt>
<dd>return only this number of accessions or NULL for no limits</dd></dl>

Arguments

Find all accessions for a taxa — getAccessions

<dl>

<dt>taxaId</dt>
<dd>a vector of taxonomic IDs</dd>


<dt>sqlFile</dt>
<dd>a string giving the path to a SQLite file created by <code>read.accession2taxid</code></dd>


<dt>version</dt>
<dd>either 'version' indicating that taxaids are versioned e.g. Z17427.1 or 'base' indicating that taxaids do not have version numbers e.g. Z17427</dd>


<dt>limit</dt>
<dd>return only this number of accessions or NULL for no limits</dd>

</dl>

getAccessions: Find all accessions for a taxa

Description

Usage

Value

Arguments

See Also

Examples