Package: HaploCatcher 1.0.4
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_1.0.4.tar.gz
HaploCatcher_1.0.4.zip(r-4.5)HaploCatcher_1.0.4.zip(r-4.4)HaploCatcher_1.0.4.zip(r-4.3)
HaploCatcher_1.0.4.tgz(r-4.4-any)HaploCatcher_1.0.4.tgz(r-4.3-any)
HaploCatcher_1.0.4.tar.gz(r-4.5-noble)HaploCatcher_1.0.4.tar.gz(r-4.4-noble)
HaploCatcher_1.0.4.tgz(r-4.4-emscripten)HaploCatcher_1.0.4.tgz(r-4.3-emscripten)
HaploCatcher.pdf |HaploCatcher.html✨
HaploCatcher/json (API)
| # Install 'HaploCatcher' in R: |
| install.packages('HaploCatcher', repos = c('https://zjwinn.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
genesgeneticslocusmachine-learningmolecular-geneticspipelineplantbreeding
Last updated 7 months agofrom:b8ded23695. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
| R-4.5-win | OK | Sep 27 2024 |
| R-4.5-linux | OK | Oct 27 2024 |
| R-4.4-win | OK | Oct 27 2024 |
| R-4.4-mac | OK | Oct 27 2024 |
| R-4.3-win | OK | Oct 27 2024 |
| R-4.3-mac | OK | Oct 27 2024 |
Exports:auto_locuslocus_cvlocus_perm_cvlocus_predlocus_trainplot_locus_perm_cv
Dependencies:caretclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdoParalleldplyre1071evaluatefansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhathighripredisobanditeratorsKernSmoothknitrlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellypatchworkpillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6randomForestRColorBrewerRcpprecipesreshape2rlangrpartscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithrxfunyaml
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 Use in Forward Prediction | locus_train |
| Model Gene Compendium Data Set | marker_info |
| Visualize Permutation CV Results | plot_locus_perm_cv |
