Easy to use functions to visualize marker data from biparental populations. Useful for both analyzing and presenting genotypes in the ABH format.
The ABHgenotypeR R package to easily visualize and manipulate ABH genotypes.
ABHgenotypeR package provides simple imputation, error-correction and plotting capacities for genotype data. The function in this package were initially developed for the GBS/QTL analysis pipeline described in:
Furuta, Reuscher et. al., 2016 Adaption genotyping by sequencing for rice F2 populations. BMC Genomics XYZ
ABHgenotypeR package is supposed to serve as an intermediate but independent analysis tool between the TASSEL GBS pipeline and the
ABHgenotypeR provides functionalities not found in either TASSEL or
qtl in addition to visualization of genotypes as "graphical genotypes". Plotting is based on ggplot2.
CRAN V1.0.0 contains a bug which missorts markers, install from git for now
or from github:
install.packages("devtools")library(devtools)install_github("StefanReuscher/ABHgenotypeR", build_vignettes = TRUE)
for more information run:
vignette("ABHgenotypeR-vignette", package = "ABHgenotypeR")
fixed a bug were plot functions would sort markers wrongly