taxon-class: Class "taxon"

In megaptera: MEGAPhylogeny Techniques in R

Description

Class for taxonomic input parameters for megapteraProj.

Objects from the Class

Objects can be created by calls of the form taxon(ingroup, outgroup, kingdom, hybrids = FALSE, reference.rank = "auto").

Slots

ingroup

a vector of mode "character", giving species names or names of higher taxa that define the focal group.

outgroup

a vector of mode "character", giving species names or names of higher taxa that define the outgroup.

kingdom

a vector of mode "character", currently one of "Fungi", "Metazoa", or "Viridiplantae". The International Code of Nomenclature for algae, fungi, and plants (ICN) and the International Code of Zoological Nomenclature (ICZN) do not exclude the possibility that genera and species of plants/fungi/algae and animals share the same name (e.g., Prunella vulgaris). Therefore it is necessary to include the kingdom into the search term when querying GenBank.

species.list

logical indicating if slot ingroup is a list of species or a higher rank.

hybrids

logical: if TRUE, hybrids (as recognized by the regular expression "^x_|_x_") will be excluded from the pipeline.

reference.rank

a vector of mode "character", giving the name of the rank to be used to create subsets of the sequences to derive the reference sequence(s). The default ("auto") commits the selection of the reference rank to the pipeline and in most cases you should be fine using this option.

Methods

show

signature(object = "taxon"): prints taxonomic parameter setting

Author(s)

Christoph Heibl

See Also

dbPars, locus, and megapteraPars for defining of database parameters, loci, and the pipeline's parameters, respectively, and megapteraProj for the bundling of input data.

megaptera documentation built on Jan. 15, 2017, 11:19 p.m.