| add3pt | Add markers to a framework map using 3-point likelihoods |
| cleanmap | Clean map for use in QTL mapping |
| clean.mpcross | Check data format and compute summary statistics for... |
| compare_orders | Compare potential orders for linkage groups |
| computemap | Computes map distances |
| fillmiss | Fill in missing values for an mpcross object |
| findqtl | Detect a QTL peaks in a QTL profile from (composite) interval... |
| findqtl2 | Detect a second QTL in a QTL profile from (composite)... |
| fit | Fit a full model including all QTL and effects from base... |
| identifyDesign | Identify subtype of design in pedigree |
| mapcomp-all | Functions for comparison of two map orders |
| maporder | Helper function to ensure that mpcross objects are in map... |
| mpadd | Function to combine two data sets which have the same... |
| mpcalcld | Calculate linkage disequilibrium between all pairs of markers |
| mpchrrf | Return Chromosome Recombination Fractions |
| mpclean | Find Largest Complete mpcross object |
| mpcollapse | Collapse an mpcross object into a binned object |
| mpcross | Multi-parent cross object |
| mpestrf | Estimate pairwise recombination fractions between markers |
| mpexpand | Expand a binned object to one containing full marker... |
| mpgroup | Construct linkage groups using 2-point recombination fraction... |
| mpIM | (Composite) Interval Mapping for QTL detection in... |
| mpIMlm | (Composite) Interval Mapping with linear models for QTL... |
| mpimpute | Impute missing values for an mpcross object |
| mpimputerf | Impute unknown recombination fraction values |
| mpMap2gs | Export objects to Richard Mott's genome_scan |
| mp-mapdist | Conversion between recombination fractions (R) and map... |
| mpMap-internal | Internal mpMap functions |
| mpMap-output | Output mpcross objects to other file formats |
| mpMap-package | Genetic analysis in multi-parent crosses |
| mporder | Order markers within linkage groups |
| mpprob | Compute founder probabilities for multi-parent crosses |
| nai | Count how many generations of advanced intercross (AI) are in... |
| phys2gen | Estimate a genetic map based on physical map ordering in... |
| plotlink.map | Plots linkage maps |
| 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 |
| 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... |
| subset.binmpcross | Subset binned mpcross object |
| subset.mpcross | Subset mpcross object |
| subset.mpprob | Subset mpprob object |
| 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 |
