Package: HaploCatcher
Title: A Predictive Haplotyping Package
Date: 2026-06-01
Version: 2.0.1
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)
URL: https://github.com/zjwinn/HaploCatcher
BugReports: https://github.com/zjwinn/HaploCatcher/issues
Imports: parallel, doParallel, foreach, caret, ggplot2, graphics,
        knitr, patchwork, randomForest, stats
Depends: R (>= 2.10)
LazyData: true
Suggests: rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libicu-dev
Repository: https://zjwinn.r-universe.dev
Date/Publication: 2026-06-08 21:14:48 UTC
RemoteUrl: https://github.com/zjwinn/haplocatcher
RemoteRef: HEAD
RemoteSha: be020adff0d5596313708daeec28afe706a37923
NeedsCompilation: no
Packaged: 2026-10-06 10:13:10 UTC; root
Author: Zachary Winn [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1543-1527>)
Maintainer: Zachary Winn <zwinn@outlook.com>