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.

Author
Nathan Medina-Rodriguez and Angelo Santana
Date of publication
2016-07-17 14:50:39
Maintainer
Nathan Medina-Rodriguez <nathan.medina@ulpgc.es>
License
GPL (>= 2)
Version
0.9.7

View on CRAN

Man pages

alleHaplotyper
Haplotyping of a dataset composed by several families.
alleHap-package
Allele Imputation and Haplotype Reconstruction from Pedigree...
alleImputer
Imputation of missing alleles from a dataset composed by...
alleLoader
Data loading of nuclear families (in .ped format)
alleSimulator
Simulation of genetic data (alleles) and non-genetic data...

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