zoosimd: Realizes a simulation using a zooroh data set and a zooroh...

In RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

Realizes a simulation using a zooroh data set and a zooroh model

Description

Performs a simulation under a model similar too ZooRoH. It simulates the genome as a mosaic of HBD and non-HBD segments. Several non-HBD classes can be simulated. Classes with high rates (short segments from ancient ancestors) are simulated first. Then, more recent classes are subsequently added. Recent HBD segments will mask more ancient HBD segments. See details in the method published in Molecular Ecology (Druet and Gautier, 2017). Genotypes are simulated using provided allele frequencies (from the sample), their genetic distances, the number of chromosomes and the number of SNPs. These simulations do not take into account linkage disequilibrium information. This simulation tool can for instance be used to check whether there is enough information in the data set to estimate HBD segments and their partitioning in multiple classes. Note that this simulation tool is not computationally efficient.

Usage

zoosimd(simdata, simmodel, nsim, fullout = FALSE)

Arguments

simdata	The name of the zdata object created by the zoodata function.
simmodel	The name of the zmodel object created by the zoomodel function. The simulation program uses only the number of classes, their rate and their mixing coefficient (it is the same for a pre-defined model or not).
nsim	The number of simulated individuals.
fullout	Indicates whether a more detailed output is requested.

Value

The function simulates genotypes with the properties of the data set (number of SNPs, genetic map, allele frequencies) and according to the specified model (number of HBD classes, rate of the classes and proportion of mixing). The simulation is created as in Druet and Gautier (2017) and new autozygosity masks more ancient autozygosity. The output is a new zoodata object that can be analyzed with the zoorun function.

If a more detailed output is requested with the fullout parameter, then the function returns list (for instance simres) containing the zoodata, a matrix with realized inbreeding per individual, estimated at SNP positions, in the different classes (with 1 being the most ancient class (non-HBD) and the highest number corresponds to the most recent class), and a matrix containing for each individual and at each marker position the simulated class (1 for non-HBD, 2 for most ancient HBD, etc). These elements can be accessed using the simres[[1]], simres[[2]] and simres[[3]], respectively.

RZooRoH documentation built on Oct. 27, 2023, 9:07 a.m.