BLUE                    Calculate Best Linear Unbiased Estimates using
                        linear mixed model from 'nlme' package
BLUEs.pheno             Best Linear Unbiased Estimates of phenotype
GIC_4x                  Genotypic Information Coefficient for example
                        tetraploid
IBD_4x                  Identical by descent probabilities for example
                        tetraploid
PVE                     Function to determine the percentage variance
                        explained (PVE) of a (maximal) QTL model, and
                        explore sub-models.
Phenotypes_4x           Phenotypes for example tetraploid
QTLscan                 General QTL function that allows for
                        co-factors, completely randomised block designs
                        and the possibility to derive LOD thresholds
                        using a permutation test
Rec_Data_4x             Recombination data for example tetraploid
SNP_dosages.4x          SNP marker dosage data for example tetraploid
check_cofactors         Build a multi-QTL model using step-wise
                        procedure of checking genetic co-factors.
convert_mappoly_to_phased.maplist
                        Function to extract the phased map from a
                        mappoly.map object
count_recombinations    Predict recombination breakpoints using IBD
                        probabilities
estimate_GIC            Estimate the Genotypic Information Coefficient
                        (GIC)
estimate_IBD            Generate IBD probabilities from marker
                        genotypes and a phased linkage map
exploreQTL              Explore the possible segregation type of a QTL
                        peak using Schwarz Information Criterion
findPeak                Function to find the position of maximum LOD on
                        a particular linkage group
findSupport             Function to find a LOD - x support interval
                        around a QTL position
import_IBD              Import IBD probabilities as estimated by
                        TetraOrigin or PolyOrigin
impute_dosages          Re-estimate marker dosages given IBD input
                        estimated using a high error prior.
maxL_IBD                Wrapper function to run estimate_IBD function
                        over multiple error priors
meiosis_report          Generate a 'report' of predicted meiotic
                        behaviour in an F1 population
mr.ls                   Example output of meiosis report function
phased_maplist.4x       Phased maplist for example tetraploid
plotQTL                 Plot the results of QTL scan.
plotRecLS               Plot the recombination landscape across the
                        genome
qtl_LODs.4x             QTL output for example tetraploid
segList_2x              Expected segregation for all markers types of a
                        diploid cross
segList_3x              Expected segregation for all markers types of a
                        triploid cross (4 x 2)
segList_3x_24           Expected segregation for all markers types of a
                        triploid cross (2 x 4)
segList_4x              Expected segregation for all markers types of a
                        tetraploid cross
segList_6x              Expected segregation for all markers types of a
                        hexaploid cross
segMaker                Create a list of possible QTL segregation types
singleMarkerRegression
                        Run a single marker regression using marker
                        dosages
spline_IBD              Fit splines to IBD probabilities
thinmap                 Thin out map data
visualiseGIC            Visualise Genotypic Information Coefficient
visualiseHaplo          Visualise haplotypes in certain individuals in
                        a certain region
visualisePairing        Visualise pairing of parental homologues
visualiseQTLeffects     Visualise QTL homologue effects around a QTL
                        position
