Estimation of Meiotic Recombination Rates Using Marey Maps
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README.md

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MareyMap

MareyMap is an R package to estimate local recombination rates along the genome using Marey maps.

MareyMap relies on comparing the genetic and the physical maps of a given chromosome to estimate local recombination rates (given by the slope of the curve describing the relationship between both variables), a graphical method called the Marey map method introduced by A. Chakravarti in 1991. MareyMap accepts Marey map data as input (genetic and physical positions of markers for a set of chromosomes of a species) and will return local recombination rate estimates.

MareyMap has many features and possible options (detailled in the present user guideline document) including :

  • taking Marey map data from any species, including some Marey map data for a few species provided with the package;
  • estimating local recombination rates using different interpolation methods;
  • providing in an automatic way local recombination rates for any given gene (or set of genes) in the genome.

All functionalities of MareyMap are introduced on the vignette of the package.

Installing MareyMap

To install the development version from GitHub:

  1. Install the release version of devtools from CRAN with install.packages("devtools").

  2. Make sure you have a working development environment.

    • Windows: Install Rtools.
    • Mac: Install Xcode from the Mac App Store.
    • Linux: Install a compiler and various development libraries (details vary across different flavors of Linux).
  3. Then:

library(devtools)
install_github("aursiber/MareyMap")

The stable version can be installed from CRAN using:

install.packages("MareyMap")

Once installed, the package can be loaded using:

library("MareyMap")

The web application of MareyMap

A web application (a Shiny app) is available to use the functionalities of the MareyMap package in an interactive way. MareyMap Online offers a simpler version of the R package MareyMap.

The MareyMap Online Shiny app can be found at: http://lbbe-shiny.univ-lyon1.fr/MareyMapOnline/

References

Rezvoy C, Charif D, Guéguen L, Marais GAB. (2007) MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics. 23(16): 2188-9. https://doi.org/10.1093/bioinformatics/btm315

A. Siberchicot, A. Bessy, L. Guéguen, G. Marais (2017). MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps. Genome Biology and Evolution. 9(10): 2506-2509. https://doi.org/10.1093/gbe/evx178