Visualize and Parse the Output of 'BeXY'

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Documentation for package ‘bexy’ version 0.1.3

• DESCRIPTION file.
• Package NEWS.

Help Pages

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