Compare individuals' genotype data
Count proportion of matching genotypes between all pairs of individuals, to look for unusually closely related individuals.
comparegeno(cross, what=c("proportion","number","both"))cross |
An object of class |
what |
Indicates whether to return the proportion or number of matching genotypes (or both). |
A matrix whose (i,j)th element is the proportion or number of matching genotypes for individuals i and j.
If called with what="both", the lower triangle contains the
proportion and the upper triangle contains the number.
If called with what="proportion", the diagonal contains missing
values. Otherwise, the diagonal contains the number of typed markers
for each individual.
The output is given class "comparegeno" so that appropriate
summary and plot functions may be used.
Karl W Broman, broman@wisc.edu
data(listeria) cg <- comparegeno(listeria) summary(cg, 0.7) plot(cg)
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