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| mpMap-package | Genetic analysis in multi-parent crosses |
| add3pt | Add markers to a framework map using 3-point likelihoods |
| calcmpprob | Compute founder probabilities for multi-parent crosses |
| clean.mpcross | Check data format and compute summary statistics for genotypes |
| cleanmap | Clean map for use in QTL mappin |
| compare_orders | Compare potential orders for linkage groups |
| computemap | Computes map distances |
| fillmiss | Fill in missing values for an mpcross object |
| findqtl2 | Detect a second QTL in a QTL profile from (composite) interval mapping |
| fit | Fit a full model including all QTL and effects from base model |
| fit.mpqtl | Fit a full model including all QTL and effects from base model |
| gen4ped | Generate pedigrees from multi-parent designs |
| gen8ped | Generate pedigrees from multi-parent designs |
| haldaneR2X | Conversion between recombination fractions (R) and map distance (X) |
| haldaneX2R | Conversion between recombination fractions (R) and map distance (X) |
| kosambiR2X | Conversion between recombination fractions (R) and map distance (X) |
| kosambiX2R | Conversion between recombination fractions (R) and map distance (X) |
| mapcomp | Functions for comparison of two map orders |
| maporder | Helper function to ensure that mpcross objects are in map order |
| mp.mapdist | Conversion between recombination fractions (R) and map distance (X) |
| mpadd | Add markers onto an existing 'mpcross' object |
| mpcalcld | Calculate linkage disequilibrium between all pairs of markers |
| mpcross | Multi-parent cross object |
| mpcross.object | Multi-parent cross object |
| mpestrf | Estimate pairwise recombination fractions between markers |
| mpgroup | Group markers into linkage groups given 2-pt recombination fraction estimates |
| mpIM | (Composite) Interval Mapping for QTL detection in multi-parent crosses |
| mpMap | Genetic analysis in multi-parent crosses |
| mporder | Order markers within linkage groups |
| mpprob | Compute founder probabilities for multi-parent crosses |
| mpsegrat | Check data format and compute summary statistics for genotypes |
| nai | Count how many generations of advanced intercross are in a pedigree |
| plot.mapcomp | Functions for comparison of two map orders |
| plot.mpcross | Plot summary of mpcross object |
| plot.mpprob | Plot summary of founder probabilities and haplotype blocks |
| plot.mpqtl | Plot output from interval mapping with detected QTL |
| plotlink.map | Plots linkage maps |
| print.mpcross | Multi-parent cross object |
| print.mpprob | Compute founder probabilities for multi-parent crosses |
| qtlmap | Select markers in a region around QTL |
| read.mpcross | Construct mpcross objects from datafiles |
| sim.mpcross | Simulate data from multi-parent designs |
| sim.mpped | Generate pedigrees from multi-parent designs |
| sim.sigthr | Simulate a significance threshold for (composite) interval mapping |
| subset.mpcross | Subset mpcross object |
| subset.mpprob | Subset mpprob object |
| summary.mapcomp | Functions for comparison of two map orders |
| summary.mpcross | Summary of mpcross object |
| summary.mpprob | Summary of mpprob object |
| summary.mpqtl | Summary of mpqtl object |
| supportinterval | Calculate support interval for detected QTL |
| write.mpcross | Output mpcross objects to other file formats |
| write2cross | Output mpcross objects to other file formats |
| write2happy | Output mpcross objects to other file formats |