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.

Install the latest version of this package by entering the following in R:
install.packages("alleHap")
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

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.