# Linkage Map Construction using the MSTmap Algorithm

## Documentation for package ‘ASMap’ version 1.0-8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ASMap-package | Additional functions for linkage map construction and manipulation of R/qtl objects.
alignCross | Graphical linkage group identity and alignment.
breakCross | Break linkage groups of an 'qtl' cross object
combineMap | Combine linkage maps from multiple 'qtl' cross objects
fixClones | Consensus genotypes for clonal genotype groups
genClones | Find and report genotype clones
heatMap | Heat map of the estimated pairwise recombination fractions and LOD linkage between markers.
mapBC | A constructed linkage map for a backcross barley population
mapBCu | An unconstructed marker set for a backcross barley population
mapDH | A constructed linkage map for a doubled haploid wheat population
mapDHf | An unconstructed marker set for a doubled haploid wheat population
mapF2 | Simulated constructed linkage map for a self pollinated F2 barley population
mergeCross | Merge linkage groups of an 'qtl' cross object
mstmap | Extremely fast linkage map construction for 'qtl' objects using MSTmap.
mstmap.cross | Extremely fast linkage map construction for 'qtl' objects using MSTmap.
mstmap.data.frame | Extremely fast linkage map construction for data frame objects using MSTmap.
pp.init | Parameter initialization function
profileGen | Profile individual genotype statistics for an R/qtl cross object
profileMark | Profile individual marker and interval statistics for an R/qtl cross object
pullCross | Pull markers from a linkage map.
pushCross | Push markers into an established R/qtl linkage map.
pValue | P-value graph
quickEst | Very quick estimation of genetic map distances.
statGen | Individual genotype statistics for an R/qtl cross object
statMark | Individual marker and interval statistics for an R/qtl cross object
subsetCross | Subset an R/qtl object