OneMap

OneMap is a software tool designed for constructing genetic maps in experimental crosses, including full-sib, recombinant inbred lines (RILs), F2, and backcross populations. It was initially developed by Gabriel R. A. Margarido, and A. Augusto F. Garcia, with later contributions from Marcelo Mollinari, Rodrigo R. Amadeu, Cristiane H. Taniguti, and Getúlio C. Ferreira.

The software has been available on CRAN since 2007 (OneMap on CRAN) and has undergone several updates over the years. It changed substantially after version 2.0, incorporating bug fixes, new features and performance optimization, as described in Taniguti et al. 2022. Beginning with version 3.2.0 (2024), updates now focus exclusively on maintaining accessibility and functionality.

For improved efficiency, we now recommend using software developed for polyploids species, such as MAPpoly, in the following scenarios involving diploid species:

When working with only biallelic markers (e.g., SNPs).
For outcrossing full-sib (F1), F2, or backcross populations.
For datasets with a large number of markers (>5,000).
For multi-population datasets (e.g., progeny from multiple parents; see MAPpoly2 and polyOrigin).

OneMap remains the best choice if you have:

Populations derived from recombinant inbred lines (RILs).
Datasets with multiallelic or dominant markers.

If you use OneMap (version 2.0 or later), please refer to this publication.

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("Cristianetaniguti/onemap")
install.packages("onemap", repos = c('https://cristianetaniguti.r-universe.dev', 'https://cloud.r-project.org'))

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.

How to cite

If you are using OneMap versions < 2.0, please 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:

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. (2023) 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