freq: Estimate RAPD allele frequencies

In kbroman/fingers: Identifying Clusters of Related Individuals

Estimate RAPD allele frequencies

Description

Estimate the frequency of the band allele for a set of RAPD markers.

Usage

freq(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

The RAPDs are assumed to be in Hardy-Weinberg equilibrium, and so the frequency of the band allele is estimated as \hat{p} = 1-\sqrt{1-\bar{x}} where \bar{x} is the proportion of individuals showing a band.

Value

A vector of length n.mar, containing the estimated frequencies of the band allele for each RAPD marker.

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

pull.markers

Examples

data(aedes)
f <- freq(aedes)

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