ABHgenotypeR

The ABHgenotypeR R package to easily visualize and manipulate ABH genotypes.

Introduction

The 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

The ABHgenotypeR package is supposed to serve as an intermediate but independent analysis tool between the TASSEL GBS pipeline and the qtl package. ABHgenotypeR provides functionalities not found in either TASSEL or qtl in addition to visualization of genotypes as "graphical genotypes". Plotting is based on ggplot2.

Installation

Note:

CRAN V1.0.0 contains a bug which missorts markers, install from git for now

from CRAN:

install.package("ABHgenotypeR")
library(ABHgenotypeR)

or from github:

#needs "devtools"
install.packages("devtools")
library(devtools)

install_github("StefanReuscher/ABHgenotypeR", build_vignettes = TRUE)

for more information run:

vignette("ABHgenotypeR-vignette", package = "ABHgenotypeR")