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-4.5)ABHgenotypeR_1.0.1.zip(r-4.4)ABHgenotypeR_1.0.1.zip(r-4.3)
ABHgenotypeR_1.0.1.tgz(r-4.4-any)ABHgenotypeR_1.0.1.tgz(r-4.3-any)
ABHgenotypeR_1.0.1.tar.gz(r-4.5-noble)ABHgenotypeR_1.0.1.tar.gz(r-4.4-noble)
ABHgenotypeR_1.0.1.tgz(r-4.4-emscripten)ABHgenotypeR_1.0.1.tgz(r-4.3-emscripten)
ABHgenotypeR.pdf |ABHgenotypeR.html✨
ABHgenotypeR/json (API)
NEWS
| # 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 6 years agofrom:66b70b8fc8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 11 2024 |
| R-4.5-win | OK | Oct 11 2024 |
| R-4.5-linux | OK | Oct 11 2024 |
| R-4.4-win | OK | Oct 11 2024 |
| R-4.4-mac | OK | Oct 11 2024 |
| R-4.3-win | OK | Oct 11 2024 |
| R-4.3-mac | OK | Oct 11 2024 |
Exports:correctStretchescorrectUndercalledHetsimputeByFlanksplotAlleleFreqplotCompareGenosplotGenosplotMarkerDensityreadABHgenotypesreportGenoswriteABHgenotypes
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr
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 |
