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
plotAutosomalTrisomy    Plotting the autosomal trisomies
plotAutosomalTrisomyCounts
                        Plotting the autosomal trisomies: counts on
                        that scaffold
plotAutosomalTrisomyPosteriorProbabilities
                        Plotting the autosomal trisomies: posterior
                        probabilities
plotMCMCTrace           Plot the MCMC trace for a specific parameter
plotTernary             Plotting the ternary of a bexy object
plotXY                  Plotting the counts of a bexy object, colored
                        by sex karyotype
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
