get_taxonomizr_from_accession {rCRUX} | R Documentation |
This function will append taxids and taxonomy to any dataframe with a column named accession that contains NCBI accessions (technically accession versions).
get_taxonomizr_from_accession(input, accession_taxa_sql_path, organize = TRUE)
input |
a data.frame |
accession_taxa_sql_path |
the path to an accessionTaxa sql |
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.
the data.frame with taxonomy data