bexy                    Accurate Bayesian inference of sex chromosome
                        karyotypes and sex-linked scaffolds from
                        low-depth sequencing data
getPosteriorMeanRho     Getting posterior mean rho (ploidy ratio
                        parameter) for each scaffold
getPosteriorModeAutosomalTrisomy
                        Getting the posterior mode for each autosomal
                        trisomy
getPosteriorModeScaffoldTypes
                        Getting the posterior mode for each scaffold
                        type
getPosteriorModeSexKaryotypes
                        Getting the posterior mode for each sex
                        karyotype
getSamplesWithAutosomalTrisomy
                        Getting all samples classified as a certain
                        autosomal trisomy
getSamplesWithThisKaryotype
                        Getting all samples classified as a specific
                        sex karyotype
getScaffoldsWithThisType
                        Getting all scaffolds classified as a specific
                        scaffold type
plot.bexy               Plotting a bexy object. To customize the plots,
                        please call the respective plotting functions
                        directly (e.g. plotTernary, plotCounts,
                        plotBars...).
plotAutosomalTrisomy    Plotting the autosomal trisomies
plotAutosomalTrisomyCounts
                        Plotting the autosomal trisomies: counts on
                        that scaffold
plotAutosomalTrisomyPosteriorProbabilities
                        Plotting the autosomal trisomies: posterior
                        probabilities
plotBars                Plotting a barplot with the posterior
                        probabilities of each sex karyotype per sample
plotCounts              Plotting the percentage of counts mapping to
                        two scaffolds (by default a Y-linked scaffold
                        against a X-linked scaffold), colored by sex
                        karyotype
plotMCMCTrace           Plot the MCMC trace for a specific parameter
plotTernary             Plotting the ternary of a bexy object
print.bexy              Printing a bexy object
summary.bexy            Summarizing a bexy object
writePosteriorModeAutosomalTrisomies
                        Write a file with the posterior mode for each
                        autosomal trisomy
writePosteriorModeScaffoldTypes
                        Write a file with the posterior mode for each
                        scaffold type
writePosteriorModeSexKaryotypes
                        Write a file with the posterior mode for each
                        sex karyotype
