| 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 |