Linkage Map Construction using the MSTmap Algorithm


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Documentation for package ‘ASMap’ version 1.0-4

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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