dot-fastdist: Calculate Genotypic Distances

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Calculate Genotypic Distances

Description

Calculates a symmetric matrix of distances (canberra) between genotypes, based on a given genotype matrix. Each row in the 'GenotypeMatrix' represents a genotype, and each column represents a marker.

Usage

.fastdist(GenotypeMatrix)

Arguments

GenotypeMatrix

A matrix where each row represents a genotype and each column represents a marker. Genotypes should be coded as 0 for AA, 1 for AB, and 2 for BB, with 9 representing missing data.

Value

Returns a symmetric matrix of distances (canberra) between the genotypes specified in the 'GenotypeMatrix'. Row and column names of the returned matrix correspond to the row names of the 'GenotypeMatrix'.

Examples

# Simulate genotype data for 40 individuals across 1000 SNPs
genotypes <- .simulateHalfsib(numInd = 5, numSNP = 1000, recbound = 0:6, type = "genotype")
# Calculate the distance matrix
dist_matrix <- hsphase::.fastdist(genotypes)
print(dist_matrix)

hsphase documentation built on Feb. 17, 2026, 5:07 p.m.