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Additional functions for linkage map construction and manipulation of R/qtl objects.

ASMap-package.Rd

Additional functions for linkage map construction and manipulation of R/qtl objects. This includes extremely fast linkage map clustering and marker ordering using MSTmap (see Wu et al., 2008).

Details

Package:ASMap
Type:Package
Version:1.0-4
Date:2018-10-24
License:GPL 2

Welcome to the ASMap package!

One of the fundamental reasons why this package exists was to utilize and implement the source code for the the Minimum Spanning Tree algorithm derived in Wu et al. (2008) (reference below) for linkage map construction. The algorithm is lightning quick at linkage group clustering and optimal marker ordering and can handle large numbers of markers.

The package contains two very efficient functions, mstmap.data.frame and mstmap.cross, that provide users with a highly flexible set linkage map construction methods using the MSTmap algorithm. mstmap.data.frame constructs a linkage map from a data frame of genetic marker data and will use the entire contents of the object to form linkage groups and optimally order markers within each linkage group. mstmap.cross is a linkage map construction function for qtl package objects and can be used to construct linkage maps in a flexible number of ways. See ?mstmap.cross for complete details.

To complement the computationally efficient linkage map construction functions, the package also contains functions pullCross and pushCross that allow the pulling/pushing markers of different types to and from the linkage map. This system gives users the ability to initially pull markers aside that are not needed for immediate construction and push them back later if required. There are also functions for fast numerical and graphical diagnosis of unconstructed and constructed linkage maps. Specifically, there is an improved heatMap that graphically displays pairwise recombination fractions and LOD scores with separate legends for each. profileGen can be used to simultaneously profile multiple statistics such as recombination counts and double recombination counts for individual lines across the constructed linkage map. profileMark allows simultaneous graphical visualization of marker or interval statistics profiles across the genome or subsetted for a predefined set of linkage groups. Graphical identification and orientation of linkage groups using reference linkage maps can be conducted using alignCross. All of these graphical functions utilize the power of the advanced graphics package lattice to provide seamless multiple displays.

Other miscellaneous utilities for qtl objects include

  • mergeCross: Merging of linkage groups

  • breakCross: Breaking of linkage groups

  • combineMap: Combining linkage maps

  • quickEst: Very quick estimation of genetic map distances

  • genClones: Reporting genotype clones

  • fixClones: Consensus genotypes for clonal groups

Complete documentation for the package is published at https://drj001.github.io/ASMap/, as a set of articles containing detailed explanations of each function and how it may be used to perform efficient map construction. These include a fully worked example involving pre-construction diagnostics, linkage map construction and post-construction diagnostics, and extending to post-construction techniques such as fine mapping and the combining of linkage maps.

A short introduction is installed with the package and may be viewed with vignette("ASMap"). The package is succinctly described in the Journal of Statistical Software publication Taylor and Butler (2017) referenced below.

Author

Julian Taylor, Dave Butler, Timothy Close, Yonghui Wu, Stefano Lonardi Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>

References

Wu, Y., Bhat, P., Close, T.J, Lonardi, S. (2008) Efficient and Accurate Construction of Genetic Linkage Maps from Minimum Spanning Tree of a Graph. Plos Genetics, 4, Issue 10.

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

See also

qtl-package