HaploCatcher: A Predictive Haplotyping Package

Used for predicting a genotype’s allelic state at a specific locus/QTL/gene. This is accomplished by using both a genotype matrix and a separate file which has categorizations about loci/QTL/genes of interest for the individuals in the genotypic matrix. A training population can be created from a panel of individuals who have been previously screened for specific loci/QTL/genes, and this previous screening could be summarized into a category. Using the categorization of individuals which have been genotyped using a genome wide marker platform, a model can be trained to predict what category (haplotype) an individual belongs in based on their genetic sequence in the region associated with the locus/QTL/gene. These trained models can then be used to predict the haplotype of a locus/QTL/gene for individuals which have been genotyped with a genome wide platform yet not genotyped for the specific locus/QTL/gene. This package is based off work done by Winn et al 2021. For more specific information on this method, refer to <doi:10.1007/s00122-022-04178-w>.

Version: 1.0.4
Depends: R (≥ 2.10)
Imports: base, parallel, doParallel, foreach, caret, ggplot2, graphics, knitr, patchwork, lattice, randomForest
Suggests: rmarkdown, testthat (≥ 3.0.0)
Published: 2023-04-21
Author: Zachary Winn ORCID iD [aut, cre]
Maintainer: Zachary Winn <zwinn at outlook.com>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: README
CRAN checks: HaploCatcher results

Documentation:

Reference manual: HaploCatcher.pdf
Vignettes: An Introduction to HaploCatcher

Downloads:

Package source: HaploCatcher_1.0.4.tar.gz
Windows binaries: r-devel: HaploCatcher_1.0.4.zip, r-release: HaploCatcher_1.0.4.zip, r-oldrel: HaploCatcher_1.0.4.zip
macOS binaries: r-release (arm64): HaploCatcher_1.0.4.tgz, r-oldrel (arm64): HaploCatcher_1.0.4.tgz, r-release (x86_64): HaploCatcher_1.0.4.tgz
Old sources: HaploCatcher archive

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