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: 0.9.7
Imports: abind, tools, stats, utils
Suggests: knitr
Published: 2016-07-17
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
CRAN checks: alleHap results

Downloads:

Reference manual: alleHap.pdf
Vignettes: alleHap vignette
Package source: alleHap_0.9.7.tar.gz
Windows binaries: r-devel: alleHap_0.9.7.zip, r-release: alleHap_0.9.7.zip, r-oldrel: alleHap_0.9.7.zip
OS X El Capitan binaries: r-release: alleHap_0.9.7.tgz
OS X Mavericks binaries: r-oldrel: alleHap_0.9.7.tgz
Old sources: alleHap archive

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