JointGenotypeCounts {Jacquard}R Documentation

Calculate joint pairwise Genotype Counts

Description

Function JointGenotypeCounts counts for each pair of individuals in the database their nine joint genotype counts

Usage

JointGenotypeCounts(X.gen, one.is.minor = TRUE)

Arguments

X.gen

A matrix with genotype data coded in (0,1,2) format

one.is.minor

If TRUE the genotype data represent the count of the minor allele for each marker, if FALSE the major allele.

Value

A list object with nine fields containing:

f0000

Matrix of (0/0,0/0) counts for all pairs

f1111

Matrix of (1/1,1/1) counts for all pairs

f1101

Matrix of (1/1,0/1) counts for all pairs

f0111

Matrix of (0/1,1/1) counts for all pairs

f0101

Matrix of (0/1,0/1) counts for all pairs

f1100

Matrix of (1/1,0/0) counts for all pairs

f0011

Matrix of (0/0,1/1) counts for all pairs

f0100

Matrix of (0/1,0/0) counts for all pairs

f0001

Matrix of (0/0,0/1) counts for all pairs

Author(s)

Jan Graffelman (jan.graffelman@upc.edu)

References

Graffelman, J., Weir, B.S. and Goudet, J. (2024) Estimation of Jacquard's genetic identity coefficients with bi-allelic variants by constrained least-squares. Preprint at bioRxiv. doi:10.1101/2024.03.25.586682

Examples

data(SimulatedPedigree)
JC <- JointGenotypeCounts(SimulatedPedigree[1:3,1:100])
print(JC)

[Package Jacquard version 1.0.2 Index]