alleHap: Allele Imputation and Haplotype Reconstruction from Pedigree Databases

Tools to simulate alphanumeric alleles, impute genetic missing data and reconstruct non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used with simulated datasets or real databases (previously loaded in .ped format). Haplotype reconstruction can be carried out even with missing data, since the program firstly imputes each family genotype (without a reference panel), to later reconstruct the corresponding haplotypes for each family member. All this considering that each individual (due to meiosis) should unequivocally have two alleles per marker (one inherited from each parent) and thus imputation and reconstruction results can be deterministically calculated.

Version:	0.9.9
Imports:	abind, tools, stats, utils
Suggests:	knitr
Published:	2017-08-19
DOI:	10.32614/CRAN.package.alleHap
Author:	Nathan Medina-Rodriguez and Angelo Santana
Maintainer:	Nathan Medina-Rodriguez <nathan.medina at ulpgc.es>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
In views:	MissingData
CRAN checks:	alleHap results

Documentation:

Reference manual:	alleHap.pdf
Vignettes:	alleHap vignette

Downloads:

Package source:	alleHap_0.9.9.tar.gz
Windows binaries:	r-devel: alleHap_0.9.9.zip, r-release: alleHap_0.9.9.zip, r-oldrel: alleHap_0.9.9.zip
macOS binaries:	r-release (arm64): alleHap_0.9.9.tgz, r-oldrel (arm64): alleHap_0.9.9.tgz, r-release (x86_64): alleHap_0.9.9.tgz, r-oldrel (x86_64): alleHap_0.9.9.tgz
Old sources:	alleHap archive

Linking:

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