r3-package: Realized Relatedness Rtools
In bowenwang7/r3: Realized Relatedness Estimation and Simulation
Description
Details
Author(s)
References
Description
This package provides useful functions for studying realized genetic relatedness between people. Users will be able to simulate inheritance patterns given pedigree structures, generate SNP marker data given inheritance patterns, and estimate realized relatedness between pairs of individuals using SNP marker data.
Details
Given a pedigree structure and a specified chromosomal length in Haldane centiMorgan (cM), sim.recomb simulates recombination breakpoints in each meiosis under a homogeneous Poisson process of rate 0.01/cM. With founder haplotypes supplied, populate.snp populates SNP marker data on all non-founders according to output of sim.recomb. Simulation true identity by descent information can be scored using functions such as ibd.length, ibd.proportion, ibd.segment and ibd.marker.
grm.pair computes realized relatedness estimates between a pair of individuals using SNP marker data. Details on various types of GRM estimators are presented in Wang et al. (2017). When the LD-weighted GRM estimator is desired, ld.weights can be used to compute the appropirate LD weights. grm.matrix is the matrix/all-pairs version of grm.pair.
Author(s)
Bowen Wang.
Maintainer: Bowen Wang <bowenwang7@gmail.com>
References
Wang et al. (2017) Genetics 205:1063-1078, https://www.ncbi.nlm.nih.gov/pubmed/28100587.
bowenwang7/r3 documentation built on May 17, 2019, 6:39 p.m.
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Description Details Author(s) References
Description
This package provides useful functions for studying realized genetic relatedness between people. Users will be able to simulate inheritance patterns given pedigree structures, generate SNP marker data given inheritance patterns, and estimate realized relatedness between pairs of individuals using SNP marker data.
Details
Given a pedigree structure and a specified chromosomal length in Haldane centiMorgan (cM), sim.recomb simulates recombination breakpoints in each meiosis under a homogeneous Poisson process of rate 0.01/cM. With founder haplotypes supplied, populate.snp populates SNP marker data on all non-founders according to output of sim.recomb. Simulation true identity by descent information can be scored using functions such as ibd.length, ibd.proportion, ibd.segment and ibd.marker.
grm.pair computes realized relatedness estimates between a pair of individuals using SNP marker data. Details on various types of GRM estimators are presented in Wang et al. (2017). When the LD-weighted GRM estimator is desired, ld.weights can be used to compute the appropirate LD weights. grm.matrix is the matrix/all-pairs version of grm.pair.
Author(s)
Bowen Wang.
Maintainer: Bowen Wang <bowenwang7@gmail.com>
References
Wang et al. (2017) Genetics 205:1063-1078, https://www.ncbi.nlm.nih.gov/pubmed/28100587.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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