Lynch.distance: Calculate Band-Sharing Dissimilarity Between Genotypes

In polysat: Tools for Polyploid Microsatellite Analysis

Calculate Band-Sharing Dissimilarity Between Genotypes

Description

Given two genotypes in the form of vectors of unique alleles, a dissimilarity is calculated as: 1 - (number of alleles in common)/(average number of alleles per genotype).

Usage

Lynch.distance(genotype1, genotype2, usatnt = NA, missing = -9)

Arguments

genotype1	A vector containing all alleles for a particular sample and locus. Each allele is only present once in the vector.
genotype2	A vector of the same form as genotype1, for another sample at the same locus.
usatnt	The microsatellite repeat length for this locus (ignored by the function).
missing	The symbol used to indicate missing data in either genotype vector.

Details

Lynch (1990) defines a simple measure of similarity between DNA fingerprints. This is 2 times the number of bands that two fingerprints have in common, divided by the total number of bands that the two genotypes have. Lynch.distance returns a dissimilarity, which is 1 minus the similarity.

Value

If the first element of either or both input genotypes is equal to missing, NA is returned.

Otherwise, a numerical value is returned. This is one minus the similarity. The similarity is calculated as the number of alleles that the two genotypes have in common divided by the mean length of the two genotypes.

Author(s)

Lindsay V. Clark

References

Lynch, M. (1990) The similarity index and DNA fingerprinting. Molecular Biology and Evolution 7, 478-484.

See Also

Bruvo.distance, meandistance.matrix

Examples

Lynch.distance(c(100,102,104), c(100,104,108))
Lynch.distance(-9, c(102,104,110))
Lynch.distance(c(100), c(100,104,106))

polysat documentation built on Aug. 23, 2022, 5:07 p.m.