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.

AuthorNathan Medina-Rodriguez and Angelo Santana
Date of publication2016-07-17 14:50:39
MaintainerNathan Medina-Rodriguez <nathan.medina@ulpgc.es>
LicenseGPL (>= 2)
Version0.9.7

View on CRAN

Files in this package

alleHap
alleHap/inst
alleHap/inst/examples
alleHap/inst/examples/example4.ped
alleHap/inst/examples/example3.ped
alleHap/inst/examples/example1.ped
alleHap/inst/examples/example2.ped
alleHap/inst/doc
alleHap/inst/doc/alleHap.pdf
alleHap/inst/doc/alleHap.R
alleHap/inst/doc/alleHap.Rnw
alleHap/NAMESPACE
alleHap/R
alleHap/R/alleImputer.R alleHap/R/alleSimulator.R alleHap/R/alleLoader.R alleHap/R/alleHaplotyper.R
alleHap/vignettes
alleHap/vignettes/alleHap.bib
alleHap/vignettes/main_Page.tex
alleHap/vignettes/logo.png
alleHap/vignettes/alleHap.Rnw
alleHap/vignettes/inconsolata.sty
alleHap/vignettes/alleHap-concordance.tex
alleHap/MD5
alleHap/build
alleHap/build/vignette.rds
alleHap/DESCRIPTION
alleHap/man
alleHap/man/alleLoader.Rd alleHap/man/alleHaplotyper.Rd alleHap/man/alleHap-package.Rd alleHap/man/alleImputer.Rd alleHap/man/alleSimulator.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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