add3pt                  Add markers to a framework map using 3-point
                        likelihoods
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
haldaneR2X              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
mpIM                    (Composite) Interval Mapping for QTL detection
                        in multi-parent crosses
mpMap-package           Genetic analysis in multi-parent crosses
mpadd                   Add markers onto an existing 'mpcross' object
mpcalcld                Calculate linkage disequilibrium between all
                        pairs of markers
mpcross                 Multi-parent cross object
mpestrf                 Estimate pairwise recombination fractions
                        between markers
mpgroup                 Group markers into linkage groups given 2-pt
                        recombination fraction estimates
mporder                 Order markers within linkage groups
mpprob                  Compute founder probabilities for multi-parent
                        crosses
nai                     Count how many generations of advanced
                        intercross are in a pedigree
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
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.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
