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 |
| DOI: |
10.32614/CRAN.package.HaploCatcher |
| Author: |
Zachary Winn 
[aut, cre] |
| Maintainer: |
Zachary Winn <zwinn at outlook.com> |
| License: |
MIT + file LICENSE |
| NeedsCompilation: |
no |
| Materials: |
README |
| CRAN checks: |
HaploCatcher results |
Documentation:
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