get_taxonomizr_from_accession {rCRUX}

R Documentation

Attach taxonomy data to an input table

Description

This function will append taxids and taxonomy to any dataframe with a column named accession that contains NCBI accessions (technically accession versions).

Usage

get_taxonomizr_from_accession(input, accession_taxa_sql_path, organize = TRUE)

Arguments

input	a data.frame
accession_taxa_sql_path	the path to an accessionTaxa sql

Details

It takes a dataframe and searches for a column called accession. If present, the column data is passed to taxonomizr::accessionToTaxa() to find the corresponding taxids. The taxids are passed to taxonomizr::getTaxonomy() and the following taxonomic information is retrieved for each of the following ranks: species, superkingdom, kingdom, phylum, subphylum, superclass, class, subclass, order, family, subfamily, genus, infraorder, subcohort, superorder, superfamily, tribe, subspecies, subgenus, species group, parvorder, varietas. New columns for taxid and each rank are appended to the dataframe.

Value

the data.frame with taxonomy data

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