Count the number of matching genotypes between all pairs of individuals, to look for unusually closely related individuals.
compare_geno(cross, omit_x = FALSE, proportion = TRUE, quiet = TRUE, cores = 1)A square matrix; diagonal is number of observed genotypes
for each individual. The values in the lower triangle are the
numbers of markers where both of a pair were genotyped. The
values in the upper triangle are either proportions or counts
of matching genotypes for each pair (depending on whether
proportion=TRUE or =FALSE). The object is given
class "compare_geno".
Object of class "cross2". For details, see the
R/qtl2 developer guide.
If TRUE, only use autosomal genotypes
If TRUE (the default), the upper triangle of the result contains the proportions of matching genotypes. If FALSE, the upper triangle contains counts of matching genotypes.
IF FALSE, print progress messages.
Number of CPU cores to use, for parallel calculations.
(If 0, use parallel::detectCores().)
Alternatively, this can be links to a set of cluster sockets, as
produced by parallel::makeCluster().
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
cg <- compare_geno(grav2)
summary(cg)
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