ASMappackage {ASMap}  R Documentation 
Additional functions for linkage map construction and manipulation of R/qtl objects.
Description
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:  1.04 
Date:  20181024 
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
A comprehensive vignette showcasing the package is now available! It contains detailed explanations of the functions in the package and how they can be used to perform efficient map construction. There is a fully worked example that involves preconstruction diagnostics, linkage map construction and post construction diagnostics. This example also shows how functions of the package can be used for post linkage map construction techniques such as fine mapping and combining linkage maps. The vignette has be succinctly summarised in the Journal of Statistical Software publication Taylor and Butler (2017) referenced below.
Author(s)
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.