Count alleles identical by state
This function counts, for all pairs of subjects and across all SNPs, the total number of alleles which are identical by state (IBS)
ibsCount(snps, uncertain = FALSE)
snps |
An input object of class |
uncertain |
If |
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.
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.
In genome-wide studies, the SNP data will usually be held as a series of
objects (of
class "SnpMatrix" or "XSnpMatrix"), one
per chromosome. Note that the matrices
produced by applying the ibsCount function to each object in turn
can be added to yield the genome-wide result.
David Clayton dc208@cam.ac.uk
ibsDist which calculates a distance matrix based
on proportion of alleles which are IBS
data(testdata) ibs.A <- ibsCount(Autosomes[,1:100]) ibs.X <- ibsCount(Xchromosome)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.