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RZooRoH
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Download and install RZooRoH package within the R console
Install from CRAN:
install.packages("RZooRoH")
Install from Github:
library("remotes")
install_github("cran/RZooRoH")
Install by package version:
library("remotes")
install_version("RZooRoH", "0.3.2.1")
Attach the package and use:
library("RZooRoH")
Maintained by
Tom Druet
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[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-06-19
Latest Update: 2023-09-04
Description:
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>.
How to cite:
Tom Druet (2018). RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes. R package version 0.3.2.1, https://cran.r-project.org/web/packages/RZooRoH
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Functions, R codes and Examples using
the RZooRoH R package
Some associated functions: BBB_NMP_GP_subset . BBB_NMP_ad_subset . BBB_NMP_pl_subset . BBB_PE_gt_subset . BBB_samples . RZooRoH . cumhbd . genoex . genosim . probhbd . rara_mix10r . realized . rohbd . soay_mix10r . typs . typsfrq . wilt_mix10r . zoodata . zoodoris . zoomodel . zooplot_hbdseg . zooplot_individuals . zooplot_partitioning . zooplot_prophbd . zoorun . zoosimd .
Some associated R codes: data.R . lib_kl.R . lib_kr.R . lib_mixkl.R . lib_mixkr.R . prob_emission.R . read_zdata.R . zooplot_segments.R . zooroh.R . zooroh_accessor.R . zooroh_model.R . zplot_individual.R . zplot_prophbd.R . zplot_vertical.R . Full RZooRoH package functions and examples
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