| 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","both"))
cross |
An object of class cross. See
read.cross for details. |
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.
Karl W Broman, kbroman@biostat.wisc.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
hist(output, breaks=150, prob=TRUE,
xlab="Proportion of matching genotypes")
rug(output)