Package: HaploCatcher 2.0.1
Zachary Winn
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>.
Authors:
HaploCatcher_2.0.1.tar.gz
HaploCatcher_2.0.1.tar.gz(r-4.7-any)HaploCatcher_2.0.1.tar.gz(r-4.6-any)
HaploCatcher_2.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HaploCatcher/json (API)
| # Install 'HaploCatcher' in R: |
| install.packages('HaploCatcher', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zjwinn/haplocatcher/issues
- gene_comp - Model Gene Compendium Data Set
- geno_mat - Model Gene Compendium Data Set
- marker_info - Model Gene Compendium Data Set
Last updated from:8157bf9aa2. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 179 | ||
| source / vignettes | OK | 284 | ||
| linux-release-x86_64 | OK | 203 | ||
| wasm-release | OK | 149 |
Exports:auto_locuslocus_cvlocus_perm_cvlocus_predlocus_trainplot_locus_perm_cv
Dependencies:caretclasscliclockcodetoolscpp11data.tablediagramdigestdoParalleldplyre1071evaluatefarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhathighripredisobanditeratorsKernSmoothknitrlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixModelMetricsnlmennetnumDerivparallellypatchworkpillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6randomForestRColorBrewerRcpprecipesreshape2rlangrpartS7scalesshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Auto Locus: An Automated Pipeline for Locus Prediction | auto_locus |
| Model Gene Compendium Data Set | gene_comp |
| Model Gene Compendium Data Set | geno_mat |
| Haplotype Prediction: Cross Validation of KNN and RF Models | locus_cv |
| Haplotype Prediction: Permutation Cross Validation of KNN and RF Models | locus_perm_cv |
| Haplotype Prediction: Using Trained Models to Make Predictions | locus_pred |
| Haplotype Prediction: Training Models for Forward Prediction | locus_train |
| Model Gene Compendium Data Set | marker_info |
| Visualize Permutation CV Results | plot_locus_perm_cv |
