R: Visualize and Parse the Output of 'BeXY'

# Visualize and Parse the Output of 'BeXY'

## 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