Package: RZooRoH 0.3.2.1

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

Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) <doi:10.1111/mec.14324>.

Authors:Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier

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RZooRoH/json (API)

# Install 'RZooRoH' in R:
install.packages('RZooRoH', repos = c('https://tdruet.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • BBB_NMP_GP_subset - Example for "gp" format specification
  • BBB_NMP_ad_subset - Example for "ad" 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.
  • genoex - Subset of a dataset with genotypes for 20 sheeps
  • genosim - Example from a small simulated data set
  • rara_mix10r - The result of an analysis on 22 sheeps from Rasa Aragonesa population.
  • 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.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.08 score 1 stars 30 scripts 325 downloads 4 mentions 13 exports 6 dependencies

Last updated 1 years agofrom:f53f113acc. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-win-x86_64WARNINGOct 26 2024
R-4.5-linux-x86_64WARNINGOct 26 2024
R-4.4-win-x86_64WARNINGOct 26 2024
R-4.4-mac-x86_64WARNINGOct 26 2024
R-4.4-mac-aarch64WARNINGOct 26 2024
R-4.3-win-x86_64WARNINGOct 26 2024
R-4.3-mac-x86_64WARNINGOct 26 2024
R-4.3-mac-aarch64WARNINGOct 26 2024

Exports:cumhbdprobhbdrealizedrohbdzoodatazoodoriszoomodelzooplot_hbdsegzooplot_individualszooplot_partitioningzooplot_prophbdzoorunzoosimd

Dependencies:codetoolsdata.tabledoParallelforeachiteratorsRColorBrewer

The RZooRoH package

Rendered fromzooroh-vignette.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2021-05-22
Started: 2018-06-19

Readme and manuals

Help Manual

Help pageTopics
Example for "ad" format specificationBBB_NMP_ad_subset
Example for "gp" format specificationBBB_NMP_GP_subset
Example for "pl" format specificationBBB_NMP_pl_subset
Example for "gt" format specificationBBB_PE_gt_subset
A file with names or IDs for ten samples.BBB_samples
Computes the realized inbreeding coefficientcumhbd
Subset of a dataset with genotypes for 20 sheepsgenoex
Example from a small simulated data setgenosim
Extracts the HBD probabilities from the zres objectprobhbd
The result of an analysis on 22 sheeps from Rasa Aragonesa population.rara_mix10r
Extracts the realized autozygosity from the zres objectrealized
Extracts the HBD segments from the zres objectrohbd
The result of an analysis on 110 sheeps from the Soay population.soay_mix10r
Subset of a dataset with genotypes for 6 individuals from a cattle population.typs
A file with marker allele frequencies for the cattle population.typsfrq
The result of an analysis on 23 sheeps from Wiltshire population.wilt_mix10r
Read the genotype data filezoodata
Returns number of HBD segments (or genome proportion) per size bins for DoRIS.zoodoris
Define the model for the RZooRoHzoomodel
Plot HBD segments identified with the ZooROH modelzooplot_hbdseg
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_individuals
Plot the partitioning of the genome in different HBD classes for each individualzooplot_partitioning
Plot proportion of the genome associated with different HBD classeszooplot_prophbd
Run the ZooRoH modelzoorun
Realizes a simulation using a zooroh data set and a zooroh modelzoosimd