megaptera (version 1.0-0)

taxon: Definition of Species/Higher Taxa

Description

Creates a S4 class defining a taxonomic parameters for a megapteraProj.

Usage

taxon(ingroup, outgroup, kingdom, hybrids = FALSE,  reference.rank = "auto")

Arguments

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.

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.

Value

an object of class taxon

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.