JointGenotypeCounts {Jacquard} | R Documentation |
Function JointGenotypeCounts
counts for each pair of individuals in the database their
nine joint genotype counts
JointGenotypeCounts(X.gen, one.is.minor = TRUE)
X.gen |
A matrix with genotype data coded in (0,1,2) format |
one.is.minor |
If |
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 |
Jan Graffelman (jan.graffelman@upc.edu)
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
data(SimulatedPedigree)
JC <- JointGenotypeCounts(SimulatedPedigree[1:3,1:100])
print(JC)