This function counts, for all pairs of subjects and across all SNPs,
the total number of alleles which are identical by state (IBS)
Usage
ibsCount(snps, uncertain = FALSE)
Arguments
snps
An input object of class "SnpMatrix" or
"XSnpMatrix"
uncertain
If FALSE, uncertain genotypes are
ignored. Otherwise contributions are weighted by posterior probabilities
Value
If there are N rows in the input matrix, the function returns an
N*N matrix. The lower triangle contains the total number
of comparisons and the upper triangle contains the number of these
which are IBS. The diagonal contains the number of valid calls for
each subject.
Details
For each pair of subjects the function counts the total number of
alleles which are IBS. For autosomal SNPs, each locus
contributes 4 comparisons, since each subject carries two
copies. For SNPs on the X chromosome, the number of comparisons is also
4 for female:female comparisons, but is 2 for female:male
and 1 for male:male comparisons.
See Also
ibsDist which calculates a distance matrix based
on proportion of alleles which are IBS