DESCRIPTION

Package: HaploCatcher
Title: A Predictive Haplotyping Package 
Date: 2023-3-23
Version: 1.0.4
Authors@R: 
    person("Zachary", "Winn", , "zwinn@outlook.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-1543-1527"))
Description: 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>.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
URL: https://github.com/zjwinn/HaploCatcher
BugReports: https://github.com/zjwinn/HaploCatcher/issues
Imports: 
    parallel,
    doParallel,
    foreach,
    caret,
    ggplot2,
    graphics,
    knitr,
    patchwork,
    lattice,
    randomForest
Depends: 
    R (>= 2.10)
LazyData: true
Suggests: 
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr