sim_generate_gam: This function is used to generate the fully known gamete...

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

This function is used to generate the fully known gamete genotype data given the diploid donor haplotypes. It also records gamete specific crossover exchange points

Description

This function generates a single gamete given a diploid donor's two haplotypes and the number of crossovers that should occur for a given gamete First the function picks which donor haplotype corresponds to the beginning of the gamete's chromosome, using a uniform distribution Then the function assigns the genotypes from this corresponding donor hapltoype to the whole gamete When tracking the originating haplotype, we assign the 1 or 2 to the whole gamete. However, we then re-code this to 0 or 1 (by subtracting 1) and at the end re-recode these back to 1's and 2's by adding 1 For each crossover index, i, we assume between index i-1 and index i the recombination breakpoint occurs and switch the bits for the rest of the chromosome genotypes to the opposite donor haplotype or genotype compared to the one just previous by inverting the bits We repeat this when tracking the originating haplotypes, which is why we recoded them.

Usage

sim_generate_gam(donor_haplotypes, n_crossovers)

Arguments

donor_haplotypes	a data frame with the diploid donor haplotypes in two columns
n_crossovers	an integer for the number of crossovers that should occur for this gamete

Value

list with generated crossover indices by gamete (a vector of integers such taht each integer without loss of generality, i, represents an index location of a crossover exchange point, such that the crossover occured somewhere between SNP index location i-1 and i), the 0/1 encoded genotypes for each SNP position in each genotype,the haplotypes from which each SNP in each gamete originates (encoded as 1s and 2s)

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