Package index • ASMap

Construction

Linkage group clustering, optimal marker ordering and genetic distance estimation in a single pass, using the MSTmap algorithm. Both functions are methods of the mstmap() generic and share the full set of MSTmap parameters, differing only in their input.

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.

Pre-construction

Diagnosis and curation of genotypes and markers before a map is built.

Genotype diagnostics

statGen(): Individual genotype statistics for an R/qtl cross object
profileGen(): Profile individual genotype statistics for an R/qtl cross object
genClones(): Find and report genotype clones
fixClones(): Consensus genotypes for clonal genotype groups

Marker and interval diagnostics

statMark(): Individual marker and interval statistics for an R/qtl cross object
profileMark(): Profile individual marker and interval statistics for an R/qtl cross object
pValue(): P-value graph

Setting markers aside

Pull markers of a given type out of the map and hold them in the cross object, rather than discarding them permanently.

pullCross(): Pull markers from a linkage map.
pp.init(): Parameter initialization function

Post-construction

Interpretation, display and manipulation of a constructed linkage map.

Display

heatMap(): Heat map of the estimated pairwise recombination fractions and LOD linkage between markers.
alignCross(): Graphical linkage group identity and alignment.

Reintroducing markers

pushCross(): Push markers into an established R/qtl linkage map.

Map manipulation

breakCross(): Break linkage groups of an qtl cross object
mergeCross(): Merge linkage groups of an qtl cross object
combineMap(): Combine linkage maps from multiple qtl cross objects
subsetCross(): Subset an R/qtl object
quickEst(): Very quick estimation of genetic map distances.

Datasets

Constructed and unconstructed marker sets used throughout the documentation. These are not lazy-loaded, so an explicit data() call is required.

mapDH: A constructed linkage map for a doubled haploid wheat population
mapDHf: An unconstructed marker set for a doubled haploid wheat population
mapBC: A constructed linkage map for a backcross barley population
mapBCu: An unconstructed marker set for a backcross barley population
mapF2: Simulated constructed linkage map for a self pollinated F2 barley population

Package

ASMap-package: Additional functions for linkage map construction and manipulation of R/qtl objects.