megaptera (version 1.0-0)

ncbiTaxonomy: NCBI Taxonomy Database

Description

Retrieve taxonomic classifiactions from the taxonomy database at the NCBI.

Usage

ncbiTaxonomy(taxon, species.list = FALSE, kingdom, trim,  parallel = FALSE, type = "SOCK")

Arguments

taxon

a character string giving the name of the clade of interest.

species.list

logical: is tax alist of species or a set of higher taxon names?

kingdom

a character string giving the kingdom to which term belongs. This in information is sometimes necessary as the lineages in different kingdoms can have identical names (e.g., Glaucidium in Metazoa and Viridiplantae) and the value of kingdom is then used for disambiguation.

trim

a character string determining if and how to drop uninformative higher ranks. The default, trim = "auto", drops all ranks higher than the rank of term. Alternatively, any existing name of a higher rank (e.g., "family", "kingdom", ...) may be given.

parallel

logical, indicating if ncbiTaxonomy should be executed serial or parallel

type

character

Value

a data frame containing the taxonomic classification of all species belonging to term, for which molecular sequence information is found at the NCBI.

References

Taxonomy Database website: http://www.ncbi.nlm.nih.gov/taxonomy

Federhen, Scott. 2012. The NCBI taxonomy databse. Nucleic Acids Research 40: DI36-DI43.

See Also

dbUpdateTaxonomy and dbReadTaxonomy for storing and retrieving taxonomic information in a megaptera project database.