add.to.population       Add additional data to a population object
assignChrToMarkers      Function that assigns a chromosome label to a
                        genetic marker
avg_map_distances       Functions to provide some descriptive
                        statistics on genetic maps
create.population       Create a population object
cross.denovo            Create a de novo genetic map from a population
                        object.
cross.saturate          Saturate an existing genetic map.
fake.population         Simulate a population object.
find.diff.expressed     Finding differentially expressed genes.
find.mixups             Find sample mix-ups
generate.biomarkers     Generate discrete biomarkers from the
                        continuous phenotypes
markerPlacementPlot     Plot number of markers selected.
markersCorPlot          Plotting correlation between markers on two
                        maps.
pheno2geno              Pheno2Geno - High-throughput generation of
                        genetic markers and maps from molecular
                        phenotypes
plotChildrenExpression
                        Plotting routine for children expression data.
plotMapComparison       Plotting routine for comparison of two genetic
                        maps.
plotMarkerDistribution
                        plotMarkerDistribution
plotParentalExpression
                        Plotting routine for parental expression data.
power.plot              Comparison of power of qtl detection.
projectOldMarkers       Plotting routine which shows where markers from
                        original map are located on saturated map.
pull.biomarkers         Extract the detected biomarkers from a
                        population object.
qtl.comparison.plot     Comparison of qtl profiles.
read.population         Loading genotype and phenotype data
reduceChromosomesNumber
                        Change the number of chromosomes in a cross
                        object
reorganizeMarkersWithin
                        Reorganize markers within cross object.
save.gff                Saving gff files.
scan.qtls               Scan qtls
set.geno.from.cross     Pull genotype from an object of class cross.
showRPpval              Visualize the outcome of a Rank product
                        analysis
testCross               Test cross object
testPopulation          Test population object
transformation          Basic functions to do transformation /
                        normalization of phenotypes.
write.population        Writes a population object to file.
