Distance matrix based on identity by state (IBS)

Description

Expresses a matrix of IBS counts (see ibsCount) as a distance matrix. The distance between two samples is returned as the proportion of allele comparisons which are not IBS.

Usage

ibsDist(counts)

Arguments

Value

An object of class "dist" (see dist)

Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

See Also

ibsCount, dist

Examples

data(testdata)
ibs <- ibsCount(Xchromosome)
distance <- ibsDist(ibs)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(chopsticks)
Loading required package: survival
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chopsticks/ibsDist.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ibsDist
> ### Title: Distance matrix based on identity by state (IBS)
> ### Aliases: ibsDist
> ### Keywords: cluster
> 
> ### ** Examples
> 
> data(testdata)
> ibs <- ibsCount(Xchromosome)
> distance <- ibsDist(ibs)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>