comparegeno: Compare individuals' genotype data
In byandell/qtl: Tools for analyzing QTL experiments

Description Usage Arguments Value Author(s) See Also Examples

Count proportion of matching genotypes between all pairs of individuals, to look for unusually closely related individuals.

1	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

nmissing

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)