Introduction | An example workflow | Reading in genotype files | The genotype list object | Creating graphical genotypes | Imputation of missing genotypes | Error corrections
Package: ABHgenotypeR 1.0.1
ABHgenotypeR: Easy Visualization of ABH Genotypes
Easy to use functions to visualize marker data from biparental populations. Useful for both analyzing and presenting genotypes in the ABH format.
Authors:
ABHgenotypeR_1.0.1.tar.gz
ABHgenotypeR_1.0.1.zip(r-4.7-any)ABHgenotypeR_1.0.1.zip(r-4.6-any)ABHgenotypeR_1.0.1.zip(r-4.5-any)
ABHgenotypeR_1.0.1.tgz(r-4.6-any)ABHgenotypeR_1.0.1.tgz(r-4.5-any)
ABHgenotypeR_1.0.1.tar.gz(r-4.7-any)ABHgenotypeR_1.0.1.tar.gz(r-4.6-any)
ABHgenotypeR_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ABHgenotypeR/json (API)
| # Install 'ABHgenotypeR' in R: |
| install.packages('ABHgenotypeR', repos = c('https://stefanreuscher.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stefanreuscher/abhgenotyper/issues
Last updated from:66b70b8fc8. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 164 | ||
| source / vignettes | OK | 156 | ||
| linux-release | OK | 122 | ||
| macos-release | OK | 174 | ||
| macos-oldrel | OK | 170 | ||
| windows-devel | OK | 65 | ||
| windows-release | OK | 82 | ||
| windows-oldrel | OK | 84 | ||
| wasm-release | OK | 91 |
Exports:correctStretchescorrectUndercalledHetsimputeByFlanksplotAlleleFreqplotCompareGenosplotGenosplotMarkerDensityreadABHgenotypesreportGenoswriteABHgenotypes
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecyclemagrittrplyrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ABHgenotypeR: A package for easy visualization and manipulating of ABH genotypes. | ABHgenotypeR-package ABHgenotypeR |
| Correct short miscalled stretches based on flanking alleles. | correctStretches |
| Correct undercalled heterozygous sites based on flanking alleles. | correctUndercalledHets |
| Impute missing genotypes based on flanking alleles | imputeByFlanks |
| Plot the parental allele frequencies along the chromosomes. | plotAlleleFreq |
| Compare to genotype matrices | plotCompareGenos |
| Plot graphical genotypes. | plotGenos |
| Plot the marker density along the chromosomes. | plotMarkerDensity |
| Read in the output of the genosToABH plugin. | readABHgenotypes |
| Report the total and relative number of each allele in a genotype object. | reportGenos |
| Export a genotype list to a .csv file. | writeABHgenotypes |