sim_assess_recomb: This function assesses the effectiveness of rhapsodi's...

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

This function assesses the effectiveness of rhapsodi's meiotic recombination discovery

Description

This function compares the simulated truth gamete specific recombination breakpoints to the rhapsodi predicted gamete specific breakpoints, producing a named list with 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 (# of true negatives), fn (# of false negatives), tp (# of true positives), fp (# of false positives)

Usage

sim_assess_recomb(true_recomb, pred_recomb, cons = FALSE)

Arguments

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
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. If FALSE, all are tp.

Value

metrics_out a named list with values for precision, recall, accuracy, specificity, fdr, fpr, true_n,pred_n, tn, fn, tp, fp

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