cutoff: Calculate cutoff for clustering with RAPD markers

In kbroman/fingers: Identifying Clusters of Related Individuals

Calculate cutoff for clustering with RAPD markers

Description

Calculate the cutoff for hierarchical cluster analysis to infer groups of related individuals with RAPD data.

Usage

cutoff(f,method=c("qu","meansib","qs","lr"),value=0.2)

Arguments

f	A vector of band allele frequencies for a set of RAPD markers.
method	The method to use to form the cutoff: a quantile of the distribution of distances among unrelated (qu), the mean distance between siblings (meansib), a quantile of the distribution of distances among siblings (qs), or the likelihood ratio for unrelateds vs. siblings (lr).
value	For method="qu" or method="qs", this should specify the quantile; for method="lr", this should specify the likelihood ratio.

Value

The cutoff (a single value).

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

cutoff.llr, freq, pull.markers, fingers

Examples

data(aedes)
f <- freq(aedes)
co1 <- cutoff(f,method="meansib")
co2 <- cutoff(f,method="qu",value=0.2)
co3 <- cutoff(f,method="qs",value=0.9)
co4 <- cutoff(f,method="lr",value=4.0)

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