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

## Documentation for package ‘RZooRoH’ version 0.4.0

- 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
cumkin | Computes the realized kinship
genoex | Subset of a dataset with genotypes for 20 sheeps
genosim | Example from a small simulated data set
hbd1 | The result of local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island.
hbd2 | The result of local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island (recent only).
kintaf_mix4l | The result of a kinship analysis on 18 cattle from the Amsterdam Island.
map1 | The map for local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island (recent only).
merge_zres | Merge several zres objects generated by zoorun
predhbd | Extracts the IBD probabilities from the kres object
probhbd | Extracts the HBD probabilities from the zres object
rara_mix10l | 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_mix10l | 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.
update_zres | Update one main zres object with new results
wilt_mix10l | The result of an analysis on 23 sheeps from Wiltshire population.
zoodata | Read the genotype data file
zookin | Use the ZooRoH model to estimate kinship between pairs of individuals
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