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.


ABHgenotypeR

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

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.

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:

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

for more information run:

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

News

ABHgenotypeR V1.0.1

fixed a bug were plot functions would sort markers wrongly

ABHgenotypeR V1.0.0

Release version

Reference manual

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install.packages("ABHgenotypeR")

1.0.1 by Stefan Reuscher, 2 years ago


http://github.com/StefanReuscher/ABHgenotypeR


Report a bug at http://github.com/StefanReuscher/ABHgenotypeR/issues


Browse source code at https://github.com/cran/ABHgenotypeR


Authors: Stefan Reuscher [aut, cre], Tomoyuki Furuta [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports ggplot2, reshape2, utils

Suggests knitr, rmarkdown


See at CRAN