# Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

## Documentation for package ‘RZooRoH’ version 0.3.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

BBB_NMP_ad_subset | Example for "ad" format specification
BBB_NMP_GP_subset | Example for "gp" format specification
BBB_NMP_pl_subset | Example for "pl" format specification
BBB_PE_gt_subset | Example for "gt" format specification
BBB_samples | A file with names or IDs for ten samples.
cumhbd | Computes the realized inbreeding coefficient
genoex | Subset of a dataset with genotypes for 20 sheeps
genosim | Example from a small simulated data set
probhbd | Extracts the HBD probabilities from the zres object
rara_mix10r | The result of an analysis on 22 sheeps from Rasa Aragonesa population.
realized | Extracts the realized autozygosity from the zres object
rohbd | Extracts the HBD segments from the zres object
soay_mix10r | The result of an analysis on 110 sheeps from the Soay population.
typs | Subset of a dataset with genotypes for 6 individuals from a cattle population.
typsfrq | A file with marker allele frequencies for the cattle population.
wilt_mix10r | The result of an analysis on 23 sheeps from Wiltshire population.
zoodata | Read the genotype data file
zoodoris | Returns number of HBD segments (or genome proportion) per size bins for DoRIS.
zoomodel | Define the model for the RZooRoH
zooplot_hbdseg | Plot HBD segments identified with the ZooROH model
zooplot_individuals | Plot individual curves with proportion of the genome in each HBD class or cumulated proportion in HBD classes with rates smaller than a threshold.
zooplot_partitioning | Plot the partitioning of the genome in different HBD classes for each individual
zooplot_prophbd | Plot proportion of the genome associated with different HBD classes
zoorun | Run the ZooRoH model
zoosimd | Realizes a simulation using a zooroh data set and a zooroh model