Man pages for bexy
Visualize and Parse the Output of 'BeXY'
| bexy | Accurate Bayesian inference of sex chromosome karyotypes and... |
| dot-addLegendAutosomalTrisomy.bexy | Function to create a legend for autosomal trisomy |
| dot-addLegend.bexy | Function to create a legend |
| dot-getAllPossibleAutosomalTrisomy.bexy | Function that returns all possible autosomal trisomy states... |
| dot-getAllPossibleScaffoldTypes.bexy | Function that returns all possible scaffold types used in... |
| dot-getAllPossibleSexKaryotypes.bexy | Function that returns all possible sex karyotypes used in... |
| dot-getColumns.bexy | Function to extract specific columns from a data frame or... |
| dot-getIndexScaffoldAutosomalTrisomy.bexy | Function that returns the index of a given scaffold & checks... |
| dot-getIndexScaffold.bexy | Function that returns the index of a given scaffold |
| dot-getInputTernary.bexy | Function that transforms state posteriors of sex karyotype to... |
| dot-getSamplesToHighlightAutosomalTrisomy.bexy | Function to select samples that should be highlighted for... |
| dot-getSamplesToHighlight.bexy | Function to select samples that should be highlighted |
| dot-getScaffoldNames.bexy | Function that returns the scaffold names of z |
| dot-getStringWidth.bexy | Function to get the width of a string on the current plotting... |
| dot-openFile.bexy | Function to open a file and generate error message if it was... |
| dot-plotAutosomalTrisomy.bexy | Function to plot counts of a specific autosome and color them... |
| dot-plotTernaryAndTicTacToe.bexy | Function to plot ternary plot with 7-cell plots displaying... |
| dot-plotTernary.bexy | Function to plot a ternary plot of the probabilities for... |
| dot-plotTicTacToeWithCoordinates.bexy | Function to plot a single 7-cell plot displaying posterior... |
| dot-plotXVsY.bexy | Function to plot X vs Y counts and color them according to... |
| dot-renameHeader.bexy | Function to reformat column names |
| getPosteriorMeanRho | Getting posterior mean rho (ploidy ratio parameter) for each... |
| 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 |
| 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... |
| plot.bexy | Plotting a bexy object. To customize the plots, please call... |
| plotCounts | Plotting the percentage of counts mapping to two scaffolds... |
| 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... |
| writePosteriorModeScaffoldTypes | Write a file with the posterior mode for each scaffold type |
| writePosteriorModeSexKaryotypes | Write a file with the posterior mode for each sex karyotype |
