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 |