BLUE                    Calculate Best Linear Unbiased Estimates using
                        linear mixed model from 'nlme' package
BLUEs.pheno             A data-frame of best linear unbiased predicted
                        (BLUE) phenotypes (4x)
GIC_4x                  A list of GIC estimates (4x)
IBD_4x                  A list of identity-by-descent probabilities
                        (4x)
PVE                     Function to determine the percentage variance
                        explained (PVE) of a (maximal) QTL model, and
                        explore sub-models.
Phenotypes_4x           A data-frame of phenotypes (4x)
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             A list of recombination count data (4x)
SNP_dosages.4x          A matrix of SNP marker dosages (4x)
bx                      Rcpp internal function Backward from
                        forward-backward algorithm
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
fx                      Rcpp internal function Forward from
                        forward-backward algorithm
hexa.list               A list of hexaploid bivalent pairing
                        configurations
import_IBD              Import IBD probabilities as estimated by
                        TetraOrigin
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                   A list of pairing predictions (4x)
phased_maplist.4x       A list of phased maps (4x)
plotLinearQTL           Plot the results of genome-wide QTL analysis
                        along a single track
plotLinearQTL_list      Overlay the results of a number of genome-wide
                        QTL analysis for which significance thresholds
                        are available.
plotQTL                 Plot the results of a previous QTL analysis
plotRecLS               Plot the recombination landscape across the
                        genome
polyqtlR                QTL analysis in polyploid species using
                        identity-by-descent probabilities
qtl_LODs.4x             A list of QTL results (4x)
rem.hex                 Redundant genotype classes in hexavalent
                        transition matrix (6x)
rem.quad                Redundant genotype classes in quadrivalent
                        transition matrix (4x)
segList_2x              A list of all possible bi-allelic QTL
                        segregation types (2x)
segList_3x              A list of all possible bi-allelic QTL
                        segregation types (3x)
segList_4x              A list of all possible bi-allelic QTL
                        segregation types (4x)
segList_6x              A list of all possible bi-allelic QTL
                        segregation types (6x)
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
