alleledist: Shared allele distance for diploid loci

In prabclus: Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

Shared allele distance for diploid loci

Description

Shared allele distance for codominant markers (Bowcock et al., 1994). One minus proportion of alleles shared by two individuals averaged over loci (loci with missing values for at least one individual are ignored).

Usage

  alleledist(allelelist,ni,np,count=FALSE)

Arguments

allelelist	a list of lists. In the "outer" list, there are np lists, one for each locus. In the "inner" list, for every individual there is a vector of two codes (typically characters, see alleleinit) for the two alleles in that locus. Such a list can be constructed by unbuild.charmatrix out of the charmatrix component of an output object of alleleinit.
ni	integer. Number of individuals.
np	integer. Number of loci.
count	logical. If TRUE, the number of the individual to be processed is printed.

Value

A symmetrical matrix of shared allele distances between individuals.

Author(s)

Christian Hennig [e-mail] https://www.unibo.it/sitoweb/christian.hennig/en

References

Bowcock, A. M., Ruiz-Linares, A., Tomfohrde, J., Minch, E., Kidd, J. R., Cavalli-Sforza, L. L. (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368, 455-457.

See Also

alleleinit, unbuild.charmatrix

Examples

  data(tetragonula)
  tnb <-
  coord2dist(coordmatrix=tetragonula.coord[1:50,],cut=50,file.format="decimal2",neighbors=TRUE)
  ta <- alleleconvert(strmatrix=tetragonula[1:50,])
  tai <- alleleinit(allelematrix=ta,neighborhood=tnb$nblist,distance="none")
  str(alleledist((unbuild.charmatrix(tai$charmatrix,50,13)),50,13)) 

prabclus documentation built on Oct. 24, 2023, 1:06 a.m.