oocyte data imputation

sim_assess_phasing

R Documentation

This function assesses the effectiveness of rhapsodi's diploid donor haplotype phasing

Description

This function compares the simulated truth diploid donor haplotypes to the rhapsodi predicted phased data, producing a named list of values for lhs (largest haplotype segment), ser (switch error rate), acc (accuracy), com (completeness)

Usage

sim_assess_phasing(true_donor_haps, pred_donor_haps, num_snps)

Arguments

`true_donor_haps`	a data frame of phased donor haplotypes from the generative model with column names of `donor1` and `donor2`
`pred_donor_haps`	a tibble of phased donor haplotypes from rhapsodi with column names `index`, `pos` (for SNP positions), `h1` (haplotype 1) & `h2` (haplotype 2)
`num_snps`	the number of SNPs, should be equal to the number of rows of `true_donor_haps` or `pred_donor_haps`