sim_hamming_distance_ignoreNA: This function computes the hamming distance (or the opposite...

In mccoy-lab/rhapsodi: R haploid sperm/oocyte data imputation

This function computes the hamming distance (or the opposite of accuracy), ignoring NAs rather than penalizing for their presence

Description

This function computes the hamming distance by finding mismatches between the truth and prediction, but ignoring NAs We divide the number of mismatches by the number of SNPs and return this ratio multiplied by 100 Accuracy can be found by subtracting the returned value(s) from 100 Note that this function works for vectors of haplotypes or for matrices with multiple haplotypes. In the first case, we return a single value. In the latter case, we return a vector of values.

Usage

sim_hamming_distance_ignoreNA(truth, predicted, num_snps)

Arguments

truth	either a vector of true genotypes or a matrix with multiple vectors of true genotypes, where genotypes are encoded as 0/1
predicted	either a vector of rhapsodi precited genotyptes or a matrix with multiple vectors of rhapsodi predicted genotypes, dimension matching that of truth, and genotypes are encoded as 0/1
num_snps	an integer, the number of SNPs, or the number of genotypes/length of the haplotype(s)

Value

to_return numeric(s), in percentage format, if truth & predicted are vectors, to_return is a single value; else if the inputs are matrices, to_return is a vector where the value of to_return is the hamming distance

mccoy-lab/rhapsodi documentation built on July 27, 2022, 3:56 a.m.