countIBS: calculates counts of 0, 1 and 2 IBS

Description Usage Arguments Value Author(s) Examples

Description

Returns counts of the number of markers at which a pair of subjects shares 0, 1 or 2 alleles identical-by-state (IBS), for all possible pairs. Counts for a given pair exclude markers where either pair member is missing data.

Usage

1

Arguments

x

An object of type snp.matrix

Value

IBS0

An upper triangular matrix whose (i,j)th element (i<j) is the count of non-missing markers where the ith and jth subjects share 0 alleles IBS.

IBS1

An upper triangular matrix whose (i,j)th element (i<j) is the count of non-missing markers where the ith and jth subjects share 1 allele IBS.

IBS2

An upper triangular matrix whose (i,j)th element (i<j) is the count of non-missing markers where the ith and jth subjects share 2 alleles IBS.

Author(s)

Annick Joelle Nembot-Simo, Jinko Graham and Brad McNeney

Examples

1
2
data(Nhlsim)
countIBS(Nhlsim$snp.data[1:5,])

CrypticIBDcheck documentation built on May 2, 2019, 7:30 a.m.