ABHgenotypeR: Easy Visualization of ABH Genotypes

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Easy to use functions to visualize marker data from biparental populations. Useful for both analyzing and presenting genotypes in the ABH format.

Author
Stefan Reuscher [aut, cre], Tomoyuki Furuta [aut]
Date of publication
2016-02-04 11:27:29
Maintainer
Stefan Reuscher <reuscher.stefan@gmail.com>
License
GPL-3
Version
1.0.1
URLs

View on CRAN

Man pages

ABHgenotypeR
ABHgenotypeR: A package for easy visualization and...
correctStretches
Correct short miscalled stretches based on flanking alleles.
correctUndercalledHets
Correct undercalled heterozygous sites based on flanking...
imputeByFlanks
Impute missing genotypes based on flanking alleles
plotAlleleFreq
Plot the parental allele frequencies along the chromosomes.
plotCompareGenos
Compare to genotype matrices
plotGenos
Plot graphical genotypes.
plotMarkerDensity
Plot the marker density along the chromosomes.
readABHgenotypes
Read in the output of the genosToABH plugin.
reportGenos
Report the total and relative number of each allele in a...
writeABHgenotypes
Export a genotype list to a .csv file.

Files in this package

ABHgenotypeR
ABHgenotypeR/inst
ABHgenotypeR/inst/extdata
ABHgenotypeR/inst/extdata/preprefall025TestData.csv
ABHgenotypeR/inst/doc
ABHgenotypeR/inst/doc/ABHgenotypeR-vignette.Rmd
ABHgenotypeR/inst/doc/ABHgenotypeR-vignette.html
ABHgenotypeR/inst/doc/ABHgenotypeR-vignette.R
ABHgenotypeR/NAMESPACE
ABHgenotypeR/NEWS.md
ABHgenotypeR/R
ABHgenotypeR/R/reportGenos.R
ABHgenotypeR/R/plotGenos.R
ABHgenotypeR/R/plotCompareGenos.R
ABHgenotypeR/R/correctStretches.R
ABHgenotypeR/R/ABHgenotypeR.R
ABHgenotypeR/R/imputeByFlanks.R
ABHgenotypeR/R/readABHgenotypes.R
ABHgenotypeR/R/writeABHgenotypes.R
ABHgenotypeR/R/plotMarkerDensity.R
ABHgenotypeR/R/plotAlleleFreq.R
ABHgenotypeR/R/correctUndercalledHets.R
ABHgenotypeR/vignettes
ABHgenotypeR/vignettes/ABHgenotypeR-vignette.Rmd
ABHgenotypeR/README.md
ABHgenotypeR/MD5
ABHgenotypeR/build
ABHgenotypeR/build/vignette.rds
ABHgenotypeR/DESCRIPTION
ABHgenotypeR/man
ABHgenotypeR/man/correctUndercalledHets.Rd
ABHgenotypeR/man/plotCompareGenos.Rd
ABHgenotypeR/man/reportGenos.Rd
ABHgenotypeR/man/plotAlleleFreq.Rd
ABHgenotypeR/man/readABHgenotypes.Rd
ABHgenotypeR/man/writeABHgenotypes.Rd
ABHgenotypeR/man/ABHgenotypeR.Rd
ABHgenotypeR/man/plotGenos.Rd
ABHgenotypeR/man/correctStretches.Rd
ABHgenotypeR/man/imputeByFlanks.Rd
ABHgenotypeR/man/plotMarkerDensity.Rd