R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis

TL;DR

The paper introduces the ASMap R package, which provides efficient tools for constructing, diagnosing, and repairing genetic linkage maps using the MSTmap algorithm, demonstrated on barley data.

Contribution

It presents a new R package that integrates linkage map construction, diagnosis, and post-processing tools, filling a gap in R-based genetic analysis software.

Findings

Efficient linkage map construction demonstrated on barley data

Tools for diagnosing and repairing linkage maps included

Supports post-construction techniques like fine mapping

Abstract

Although various forms of linkage map construction software are widely available, there is a distinct lack of packages for use in the R statistical computing environment. This article introduces the ASMap linkage map construction R package which contains functions that use the efficient MSTmap algorithm for clustering and optimally ordering large sets of markers. Additional to the construction functions, the package also contains a suite of tools to assist in the rapid diagnosis and repair of a constructed linkage map. The package functions can also be used for post linkage map construction techniques such as fine mapping or combining maps of the same population. To showcase the efficiency and functionality of ASMap, the complete linkage map construction process is demonstrated with a high density barley backcross marker data set.