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)