The R Journal: accepted article

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Allele Imputation and Haplotype Determination from Databases Composed of Nuclear Families PDF download
Nathan Medina-Rodríguez and Ángelo Santana

Abstract alleHap is a package designed for imputing genetic missing data and reconstruct non recombinant haplotypes from pedigree databases in a deterministic way. When genotypes of related individuals are available in a number of linked genetic markers, the program starts by identifying haplotypes compatible with the observed genotypes in those markers without missing values. If haplotypes are identified in parents or offspring, missing alleles can be imputed in subjects containing missing values. Several scenarios are analyzed: family completely genotyped, children partially genotyped and parents completely genotyped, children fully genotyped and parents containing entirely or partially missing genotypes, and founders and their offspring both only partially genotyped. alleHap also has a function to simulate pedigrees including all these scenarios. This article describes in detail how our package works for the desired applications, including illustrated explanations and easily reproducible examples.

Received: 2016-08-25; online 2017-11-16
CRAN packages: haplo.ccs, haplo.stats, hsphase, linkim, rrBLUP, synbreed, alleHap , CRAN Task Views implied by cited CRAN packages: Genetics


CC BY 4.0
This article is licensed under a Creative Commons Attribution 4.0 International license.

@article{RJ-2017-057,
  author = {Nathan Medina-Rodríguez and Ángelo Santana},
  title = {{Allele Imputation and Haplotype Determination from Databases
          Composed of Nuclear Families}},
  year = {2017},
  journal = {{The R Journal}},
  url = {https://journal.r-project.org/archive/2017/RJ-2017-057/index.html}
}