Estimate Genotyping Error Rate

This function calculates the genotyping error rate by comparing the original genotype matrix to the HMM-processed genotype matrix. The error rate is defined as the proportion of genotype mismatches, ignoring missing values. Designed to estimate error rate after haplotype_reconstruction.

Usage

estimate_error(original_geno, processed_geno)

Arguments

original_geno

A numeric genotype matrix where:

• Rows represent genetic markers.

• Columns represent individuals.

• Values are expected to be 0, 1, 2, or NA for missing data.

processed_geno

A numeric genotype matrix of the same dimensions as original_geno, containing genotypes that have been processed. Likely the output of haplotype_reconstruction. The estimated error rate could be used in haplotype_reconstruction for a more accurate estimate of

Value

A numeric value representing the estimated genotyping error rate.

Examples

if (FALSE) { # \dontrun{
# Example genotype matrices
original <- matrix(c(0, 1, 2, NA, 1, 2, 0, 1, 2, 2, NA, 1),
                   nrow = 4, ncol = 3)
processed <- matrix(c(0, 1, 1, NA, 1, 2, 0, 2, 2, 2, NA, 1),
                    nrow = 4, ncol = 3)

# Estimate genotyping error
error_rate <- estimate_error(original, processed)
print(error_rate)
} # }