| comparegeno {qtl} | R Documentation |
Count proportion of matching genotypes between all pairs of individuals, to look for unusually closely related individuals.
comparegeno(cross, what=c("proportion","number"))
cross |
An object of class cross. See
read.cross for details. |
what |
Indicates whether to return the proportion or number of matching genotypes. |
A matrix whose (i,j)th element is the proportion or number of matching genotypes for individuals i and j.
Karl W Broman, kbroman@jhsph.edu
data(listeria)
output <- comparegeno(listeria)
# image of the proportions
n.ind <- nind(listeria)
image(1:n.ind, 1:n.ind, output, col=gray((0:99)/99),
breaks=seq(0,1,len=101))
# histogram of the off-diagonal values
upper <- output[upper.tri(output)]
hist(upper, breaks=150,
xlab="Proportion of matching genotypes")
rug(upper)