sim_assess_it: This function drives the assessment of all 3 parts of...

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

This function drives the assessment of all 3 parts of rhapsodi: phasing, gamete imputation, recombination discovery

Description

This function drives all 3 steps of assessment in comparing the simulated full truth data with the rhapsodi predicted data First it assesses donor haplotypte phasing, producing a named list with single values for lhs (largest haplotype segment), ser (switch error rate), acc (accuracy), com (completeness) Then it assesses gamete genotype imputation, producing a named list with vectors for lhs (largest haplotype segment), ser (switch error rate), acc (accuracy), com (completeness) Then it assesses recombination discovery producing a named list with single values for precision, recall, accuracy, specificity, fdr (false discovery rate), fpr (false positive rate) f1 (f1 score), true_n (number of true recombination breakpoints), pred_n (number of predicted recombination breakpoints), tn (true negative), fn (false negative), tp (true positive), fp (false positive) Finally, it returns a list of named lists where phasing contains the phasing assessment named list gam_imputation contains the gamete genotype imputation assessment named list and recomb contains the recombination breakpoint discovery assessment named list

Usage

sim_assess_it(
  true_donor_haps,
  pred_donor_haps,
  true_recomb,
  pred_recomb,
  true_gam,
  pred_gam,
  cons = FALSE,
  verbose = FALSE
)

Arguments

true_donor_haps	a data frame of phased donor haplotypeps 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)
true_recomb	a data.table data table containing the true recombination breakpoints from the generative model with columns gam, start, end
pred_recomb	a tibble containing the predicted recombination breakpoints from rhapsodi with columns Ident, Genomic_start, Genomic_end
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, the predicted/filled gamete genotypes where the rows are the SNPs and the columns are the gametes
cons	a bool; default=FALSE, If TRUE, compares recombination breakpoints in a conservative manner such that if two or more true breakpoints intersect a single predicted breakpoint, we only consider one intersection to be a tp and the rest to be fn.
verbose	a bool; default is FALSE; if TRUE, prints progress statements after each step is successfully completed

Value

all_metrics a named list of named lists with all the assessment metric values or vectors

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