calc.dist: Calculate simple distance matrix

In kbroman/fingers: Identifying Clusters of Related Individuals

Calculate simple distance matrix

Description

Calculate the simple distance matrix, by the proportion of mismatches, for a RAPD data set.

Usage

calc.dist(dat)

Arguments

dat	A matrix of size (n.ind x n.mar) containing RAPD phenotypes, with 1 indicating the presence of a band and 0 indicating absence.

Details

For each pair of individuals, we calculate the proportion of RAPD markers (among those where both individuals have complete data) at which one individual shows a band and the other doesn't.

Value

A symmetric matrix of dimension (n.ind x n.ind), containing the distances between individuals.

Author(s)

Karl W Broman [e-mail]

References

BL Apostol, WC Black IV, BR Miller, P Reiter, BJ Beaty (1993) Estimation of the number of full sibling families at an oviposition site using RAPD-PCR markers: applications to the mosquito Aedes aegypti. Theor Appl Genet 86:991-1000.

See Also

llrdist, fingers

Examples

data(aedes)
d <- calc.dist(aedes)

kbroman/fingers documentation built on May 17, 2023, 11:50 p.m.