OneMap

OneMap is a software for constructing genetic maps in experimental crosses: full-sib, RILs, F2, and backcrosses. It was developed by Gabriel R A Margarido, Marcelo Mollinari and A Augusto F Garcia. Later on, Rodrigo R Amadeu, Cristiane H Taniguti, and Getulio C. Ferreira joined the project.

It has been available on CRAN for several years (https://cran.r-project.org/package=onemap). Its last version was updated on 2020-02-17. CRAN has OneMap's stable version, which is recommended for most users.

This GitHub page has its version under development. New functions will be added (experimental work) and, once it is done, we will synchronize the repositories and add them to CRAN.

We worked very hard to release a new stable version allowing users to analyze data sets with markers based on sequencing technologies, such as Illumina, GBS, etc.

OneMap comprises a set of functions that allow users to build a linkage map. Some functions are used internally by the package, and should not be used directly.

How to install

From CRAN (stable version)

It is easy, just type (within R):

setRepositories(ind = 1:2)
install.packages("onemap", dependencies=TRUE)

You also can use the console menus: Packages -> Install package(s). After clicking, a box will pop-up asking you to choose the CRAN mirror. Choose the location nearest to you. Then, another box will pop-up asking you to choose the package you want to install. Select onemap then click OK. The package will be automatically installed on your computer.

OneMap can also be installed by downloading the appropriate files directly at the CRAN website and following the instructions given in section 6.3 Installing Packages of the R Installation and Administration manual.

From github (version under development)

Within R, you need to install and load the package devtools:

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

This will allow you to automatically build and install packages from GitHub. If you use Windows, first install Rtools. If you are facing problems with Rtools installation, try to do it by selecting the Run as Administrator option with the right mouse button. On a Mac, you will need Xcode (available on the App Store).

Then, to install OneMap from GitHub (this very repo):

install_github("augusto-garcia/onemap")

From docker hub

OneMap requires several dependencies that you may not have in your system. To overcome the need of installing all of them, you can use the OneMap image in the docker hub. Install docker (see more about here) and use:

docker pull cristaniguti/onemap_git:latest

The OneMap image already has the RStudio from rocker image, you can run it in your favorite browser running the following command:

docker run -p 8787:8787 -v $(pwd):/home/rstudio/ -e DISABLE_AUTH=true cristaniguti/onemap_git

This will make the container available in port 8787 (choose other if you prefer). The -v argument includes directories of your computer, in this case, the current directory (pwd) to the container. You can use -v several times to include several directories. After, you just need to go to your favorite browser and search for <your_localhost>:8787 (example 127.0.0.1:8787). That is it! Everything you need is there.

Tutorials

You can read OneMap tutorials going to the vignettes of the installed package, or clicking below. Please, start with the overview, that will guide you through other chapters.

1. Overview

2. Introduction to R

3. How to build a linkage map for inbred-bases populations (F2, RIL and BC)

4. How to build a linkage map for outcrossing populations

5. A guide to build high-density linkage maps

How to cite

Margarido, G. R. A., Souza, A. P., &38; Garcia, A. A. F. (2007). OneMap: software for genetic mapping in outcrossing species. Hereditas, 144(3), 78–79. https://doi.org/10.1111/j.2007.0018-0661.02000.x

• If you are using OneMap versions > 2.0, please cite also:

Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Mollinari, M., Da, G., Pereira, S., Riera-Lizarazu, O., Lau, J., Byrne, D., de Siqueira Gesteira, G., De, T., Oliveira, P., Ferreira, G. C., &; Franco Garcia, A. A. Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. BioRxiv. https://doi.org/10.1101/2022.11.24.517847

• If you used the HMM parallelization, please cite BatchMap paper too:

Schiffthaler, B., Bernhardsson, C., Ingvarsson, P. K., &; Street, N. R. (2017). BatchMap: A parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species. PLoS ONE, 12(12), 1–12. https://doi.org/10.1371/journal.pone.0189256