Jacquard (version 1.0.2)

JointGenotypeCounts: 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)

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

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.

Author

Jan Graffelman ([e-mail])

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. tools:::Rd_expr_doi("10.1101/2024.03.25.586682")

Examples

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