sim_assess_gam_imputation: This function assesses the effectiveness of rhapsodi's gamete...

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

This function assesses the effectiveness of rhapsodi's gamete imputation

Description

This function compares the simulated full truth gamete data to the rhapsodi predicted filled gamete data, producing a named list with vectors for lhs (largest haplotype segment), ser (switch error rate), acc (accuracy), com (completeness)

Usage

sim_assess_gam_imputation(true_gam, pred_gam, num_snps, num_gametes)

Arguments

true_gam	a matrix, from the output of the generative model, the true/full gamete genotypes where the rows are the SNPs and the columns are the gametes (except for the first column which is the SNP genomic positions)
pred_gam	a matrix, from the output of rhapsodi, with the predicted/filled gamete genotypes where the rows are the SNPs and the columns are the gametes
num_snps	the number of snps, should be equal to the number of rows of true_gam or pred_gam
num_gametes	the number of gametes, should be equal to the number of cols - 1 of true_gam or just the number of cols of pred_gam

Value

assess_gam a named list with vectors for acc, com, lhs, & ser

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