Visualize and Parse the Output of 'BeXY'

Documentation for package ‘bexy’ version 0.1.2

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