getId

Find a taxa by string in the NCBI taxonomy. Note that NCBI species are stored as Genus species e.g. "Bos taurus". Ambiguous taxa names will return a comma concatenated string e.g. "123,234" and generate a warning.

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

getId function

<dl><dt>taxa</dt>
<dd>a vector of taxonomic names</dd>
<dt>sqlFile</dt>
<dd>a string giving the path to a SQLite file containing a names tables</dd>
<dt>onlyScientific</dt>
<dd>If TRUE then only match to scientific names. If FALSE use all names in database for matching (potentially increasing ambiguous matches).</dd></dl>

Arguments

Find a given taxa by name — getId

<dl>

<dt>taxa</dt>
<dd>a vector of taxonomic names</dd>


<dt>sqlFile</dt>
<dd>a string giving the path to a SQLite file containing a names tables</dd>


<dt>onlyScientific</dt>
<dd>If TRUE then only match to scientific names. If FALSE use all names in database for matching (potentially increasing ambiguous matches).</dd>

</dl>

getId: Find a given taxa by name

Description

Usage

Value

Arguments

See Also

Examples