quiddich (version 1.0.0)

changesAA: Identification of diagnostic molecular characters in a nucleotide alignment that also cause diagnostic characters in the corresponding amino acid alignment

Description

This function is a tool for an automated identification of such diagnostic molecular characters in a nucleotide alignment that also cause diagnostic characters in the corresponding amino acid alignment. For each taxon given in taxOfInt, it identifies the mentioned characters and returns their positions and types in the nucleotide alignment and their positions and types in the corresponding amino acid alignment.

Usage

changesAA(DNAbin, taxVector = dimnames(DNAbin)[[1]], codonstart = 1,
  taxOfInt = "all", types = c("type1", "type2", "type3"))

Arguments

DNAbin

An object (the nucleotide alignment) of class 'DNAbin'.

taxVector

The taxon vector. Default assumes that each row in the alignment belongs to a different taxon.

codonstart

An integer defining where to start the translation of the nucleotide alignment into the corresp. amino acid alignment. Default is 1.

taxOfInt

A vector containing the taxa for which the above mentioned characters shall be extracted. Default is "all".

types

A vector containing the types of diagnostic characters (in the nucleotide alignment) that shall be considered. The types can be "all" or any combination of "type1", "type2", "type3" and "type4". Default is "type1", "type 2" and "type3".

Value

changesAA returns a list, where each entry belongs to one taxon of interest. Each taxon of interest has a matrix assigned to it, in which the first and second column contain the positions and types of the identified diagnostic characters in the nucleotide alignment and the third and fourth column contain the positions and types of the diagnostic characters in the corresponding amino acid alignment.

type1 means that the character is suitable to distinguish each individual of the taxon of interest from all individuals of the remaining taxa, and that it is fixed for one state in the taxon of interest. type2 means that the character is suitable to distinguish each individual of the taxon of interest from all individuals of the remaining taxa, and that it is not fixed for one state in the taxon of interest. type3 means that the character is suitable to distinguish some (but not all) individuals of the taxon of interest from all individuals of the remaining taxa. type4 means that the character is suitable to distinguish each individual of the taxon of interest from all individuals of at least one (but not all) other taxon while being fixed in both the taxon of interest and the compared taxa.

changesAA returns for each taxon of interest the following elements:

posDiNu

The positions of the identified diagnostic characters in the nucleotide alignment.

typeDiNu

The types of the identified diagnostic characters in the nucleotide alignment.

posDiAA

The positions of the corresponding diagnostic characters in the amino acid alignment.

typeDiAA

The types of the corresponding diagnostic characters in the amino acid alignment.

References

Kuehn, A.L., Haase, M. (2019) QUIDDICH: QUick IDentification of DIagnostic CHaracters.

Examples

# NOT RUN {
#using a dataset from spider
#install.packages("spider")
library(spider)
data("anoteropsis")
anoTax <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"),
 function(x) paste(x[1], x[2], sep="_"))
changesAA(anoteropsis, anoTax, codonstart=2, taxOfInt="all")
changesAA(anoteropsis, anoTax, codonstart=2, taxOfInt="Artoria_flavimanus",
 types="type4")

# }