Access the complete version of this vignette here
To have access to all example datasets. Install onemap
from GitHub and run the following command:
#install.packages("devtools") ## if you do not have it installed
devtools::install_github("cristianetaniguti/onemap")The following example is intended to show the usage of
OneMap functions for linkage mapping in outcrossing
(non-inbred) populations. With basic knowledge of R syntax, one should
have no problems using it. If you are not familiar with R, we recommend
reading the vignette Introduction
to R.
Hopefully, these examples will be clear enough to help any user to understand its functionality and start using it. You do not need to be an expert in R to build your linkage map, but some concepts are necessary and will help you through the process.
The software has been available on CRAN since 2007 (OneMap on CRAN) and has undergone several updates, adding new features and optimization up to version 3.2.0 in 2024. Future updates will focus solely on maintaining accessibility and functionality. New feature development and optimization efforts are now being directed toward the MAPpoly and MAPpoly2 packages.
MAPpoly is a more robust package designed for constructing linkage maps in polyploid species. Its optimized algorithms also provide improved efficiency for diploid species compared to OneMap. Therefore, we recommend using MAPpoly instead of OneMap in the following scenarios for diploid species:
However, OneMap remains the best choice if you have:
For guidance on best practices in building linkage maps while accounting for genotyping errors, please refer to Taniguti et. al 2023.