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)
NettletonDoerge         Nettleton and Doerge 2000
Nstates.fun             Error handling on ploidy and ploidy2, and
                        determine the number of genotype classes for
                        general ploidy level and pairing behaviour
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)
TM.biv.2                Bivalent-pairing transition matrix function,
                        diploid
TM.biv.4                Bivalent-pairing transition matrix function,
                        tetraploid
TM.biv.6                Bivalent-pairing transition matrix function,
                        hexaploid
TM.hex                  Hexavalent-pairing transition matrix function,
                        hexaploid
TM.quad                 Quadrivalent-pairing transition matrix
                        function, tetraploid
TMfun.2x_B              Diploid bi-parental transition matrix
TMfun.3x_BB             Triploid bi-parental transition matrix,
                        bivalent-bivalent pairing
TMfun.3x_QB             Triploid bi-parental transition matrix,
                        quadrivalent-bivalent pairing
TMfun.4x_BB             Tetraploid bi-parental transition matrix,
                        bivalent-bivalent pairing
TMfun.4x_BQ             Tetraploid bi-parental transition matrix,
                        bivalent-quadrivalent pairing
TMfun.4x_QB             Tetraploid bi-parental transition matrix,
                        quadrivalent-bivalent pairing
TMfun.4x_QQ             Tetraploid bi-parental transition matrix,
                        quadrivalent-quadrivalent pairing
TMfun.6x_BB             Hexaploid bi-parental transition matrix,
                        bivalent-bivalent pairing
TMfun.6x_BH             Hexaploid bi-parental transition matrix,
                        bivalent-hexavalent pairing
TMfun.6x_HB             Hexaploid bi-parental transition matrix,
                        hexavalent-bivalent pairing
TMfun.6x_HH             Hexaploid bi-parental transition matrix,
                        hexavalent-hexavalent pairing
bivTM                   Bivalent transition matrix function
bx                      Rcpp internal function Backward from
                        forward-backward algorithm
colour.bar              Add colour bar scale to heatplot
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
fast_IBD                Extremely fast estimation of
                        identity-by-descent (IBD) probabilities.
fast_permute            Extension of the 'QTLscan' function, offering
                        an optimised permutation test when the
                        experimental setting (i.e. phenotype structure)
                        is simple
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
hexTM                   Hexavalent transition matrix function
hexa.list               A list of hexaploid bivalent pairing
                        configurations
hmm_IBD                 Generate IBD probabilities from marker
                        genotypes and a phased linkage map using HMM
import_IBD              Import IBD probabilities as estimated by
                        TetraOrigin
impute_dosages          Re-estimate marker dosages given IBD input
                        estimated using a high error prior.
list.depth              Find depth of a list
mapseq                  Generate a sequence of map positions for
                        splining function
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
probgeno_df_to_array    Convert a progeno_df data.frame to a 3d array
qtl_LODs.4x             A list of QTL results (4x)
quadTM                  Quadrivalent transition matrix function
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
state_fun               Function to return the list of possible pairing
                        states, given parental ploidies and meiotic
                        pairing model
test_IBD_list           Error and warning handling for IBD_list as
                        estimated by 'estimate_IBD'
test_dosage_matrix      Error and warning handling for dosage_matrix
test_probgeno_df        Error and warning handling for probgeno_df
                        data-frame of probabilistic genotypes (scores)
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
weighted.var            Calculate the weighted variance
write.logheader         Write a header for the log file
