Package: alleHap 0.9.9

Nathan Medina-Rodriguez

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.

Authors:Nathan Medina-Rodriguez and Angelo Santana

alleHap_0.9.9.tar.gz
alleHap_0.9.9.tar.gz(r-4.5-noble)alleHap_0.9.9.tar.gz(r-4.4-noble)
alleHap_0.9.9.tgz(r-4.4-emscripten)alleHap_0.9.9.tgz(r-4.3-emscripten)
alleHap.pdf |alleHap.html
alleHap/json (API)

# Install 'alleHap' in R:
install.packages('alleHap', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.30 score 9 scripts 305 downloads 2 mentions 4 exports 1 dependencies

Last updated 7 years agofrom:ba6e1e87bd. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 28 2024
R-4.5-linuxOKNov 28 2024

Exports:alleHaplotyperalleImputeralleLoaderalleSimulator

Dependencies:abind

alleHap vignette

Rendered fromalleHap.Rnwusingknitr::knitron Nov 28 2024.

Last update: 2017-08-19
Started: 2015-10-05