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

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Documentation for package ‘RZooRoH’ version 0.4.0

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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