ibsCount: Count alleles identical by state

In NikNakk/snpStats: SnpMatrix and XSnpMatrix classes and methods

Description

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

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.

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.

Note

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.

Author(s)

David Clayton [e-mail]

See Also

ibsDist which calculates a distance matrix based on proportion of alleles which are IBS

Examples

data(testdata)

ibs.A <- ibsCount(Autosomes[,1:100])
ibs.X <- ibsCount(Xchromosome)

NikNakk/snpStats documentation built on May 7, 2019, 6:18 p.m.