taxonomy.table {microcontax}

Taxonomy look-up table

Description

A data frame consisting of the taxonomy information used in the ConTax data sets.

Usage

data(taxonomy.table)

Details

taxonomy.table is a data.frame consisting of the seven columns Domain, Phylum, Class, Order, Family, Genus and LPSN. The first six are taxonomy informations, the last is "Yes" or "No" indiocating if the Genus listed is also found in the List of prokaryotic names with standing in nomenclature (LPSN) database, see http://www.bacterio.net/.

Each row contains the taxonomy information for a genus, hence the number of rows equals the number of unique genera.

To quickly look-up the higher rank taxonomy for a given genus, see the function genusLookup.

Author(s)

Hilde Vinje, Kristian Hovde Liland, Lars Snipen.

See Also

genusLookup, contax.full, contax.trim, getDomain.

Examples

data(taxonomy.table)
dim(taxonomy.table)
taxonomy.table[1:10,]
genusLookup(taxonomy.table$Genus[1:10], rank = "Family")