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.
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.
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")
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.
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.
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.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092
- 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