Lynch.distance: 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)

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.

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.

Author

Lindsay V. Clark

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.

References

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

Examples

Run this code

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))

Run the code above in your browser using DataLab