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alleHap  

Allele Imputation and Haplotype Reconstruction from Pedigree Databases
View on CRAN: Click here


Download and install alleHap package within the R console
Install from CRAN:
install.packages("alleHap")

Install from Github:
library("remotes")
install_github("cran/alleHap")

Install by package version:
library("remotes")
install_version("alleHap", "0.9.9")



Attach the package and use:
library("alleHap")
Maintained by
Nathan Medina-Rodriguez
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-08-10
Latest Update: 2017-08-19
Description:
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.
How to cite:
Nathan Medina-Rodriguez (2014). alleHap: Allele Imputation and Haplotype Reconstruction from Pedigree Databases. R package version 0.9.9, https://cran.r-project.org/web/packages/alleHap. Accessed 06 Nov. 2024.
Previous versions and publish date:
0.7.2 (2014-08-10 17:40), 0.9.2 (2015-10-05 23:13), 0.9.7 (2016-07-17 14:50)
Other packages that cited alleHap R package
View alleHap citation profile
Other R packages that alleHap depends, imports, suggests or enhances
Complete documentation for alleHap
Functions, R codes and Examples using the alleHap R package
Some associated functions: alleHap-package . alleHaplotyper . alleImputer . alleLoader . alleSimulator . 
Some associated R codes: alleHaplotyper.R . alleImputer.R . alleLoader.R . alleSimulator.R .  Full alleHap package functions and examples
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