The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
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 |
Maintainer: | Zachary Winn <zwinn at outlook.com> |
License: | MIT + file LICENSE |
NeedsCompilation: | no |
Materials: | README |
CRAN checks: | HaploCatcher results |
Reference manual: | HaploCatcher.pdf |
Vignettes: |
An Introduction to HaploCatcher |
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, r-oldrel (x86_64): HaploCatcher_1.0.4.tgz |
Old sources: | HaploCatcher archive |
Please use the canonical form https://CRAN.R-project.org/package=HaploCatcher to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.