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>.
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RZooRoH_0.3.2.1.tar.gz
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RZooRoH.pdf |RZooRoH.html✨
RZooRoH/json (API)
# Install 'RZooRoH' in R: |
install.packages('RZooRoH', repos = c('https://tdruet.r-universe.dev', 'https://cloud.r-project.org')) |
- 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.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:f53f113acc. Checks:OK: 1 WARNING: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 26 2024 |
R-4.5-win-x86_64 | WARNING | Oct 26 2024 |
R-4.5-linux-x86_64 | WARNING | Oct 26 2024 |
R-4.4-win-x86_64 | WARNING | Oct 26 2024 |
R-4.4-mac-x86_64 | WARNING | Oct 26 2024 |
R-4.4-mac-aarch64 | WARNING | Oct 26 2024 |
R-4.3-win-x86_64 | WARNING | Oct 26 2024 |
R-4.3-mac-x86_64 | WARNING | Oct 26 2024 |
R-4.3-mac-aarch64 | WARNING | Oct 26 2024 |
Exports:cumhbdprobhbdrealizedrohbdzoodatazoodoriszoomodelzooplot_hbdsegzooplot_individualszooplot_partitioningzooplot_prophbdzoorunzoosimd
Dependencies:codetoolsdata.tabledoParallelforeachiteratorsRColorBrewer