bexy package - RDocumentation

getPosteriorModeSexKaryotypes

Getting the posterior mode for each sex karyotype

getPosteriorModeAutosomalTrisomy

Getting the posterior mode for each autosomal trisomy

.getAllPossibleAutosomalTrisomy.bexy

Function that returns all possible autosomal trisomy states used in BeXY

print.bexy

Printing a bexy object

plot.bexy

Plotting a bexy object. To customize the plots, please call the respective plotting functions directly (e.g. plotTernary, plotCounts, plotBars...).

writePosteriorModeSexKaryotypes

Write a file with the posterior mode for each sex karyotype

summary.bexy

Summarizing a bexy object

plotAutosomalTrisomy

Plotting the autosomal trisomies

.getAllPossibleSexKaryotypes.bexy

Function that returns all possible sex karyotypes used in BeXY

.plotTernary.bexy

Function to plot a ternary plot of the probabilities for being aneuploid, XX or XY

.openFile.bexy

Function to open a file and generate error message if it was not found

.plotTernaryAndTicTacToe.bexy

Function to plot ternary plot with 7-cell plots displaying posterior probabilities of karyotypes

.plotAutosomalTrisomy.bexy

Function to plot counts of a specific autosome and color them according to BeXY posterior mode of autosomal trisomy

plotAutosomalTrisomyCounts

Plotting the autosomal trisomies: counts on that scaffold

.addLegend.bexy

Function to create a legend

.plotXVsY.bexy

Function to plot X vs Y counts and color them according to BeXY posterior mode

getPosteriorModeScaffoldTypes

Getting the posterior mode for each scaffold type

getSamplesWithThisKaryotype

Getting all samples classified as a specific sex karyotype

.renameHeader.bexy

Function to reformat column names

writePosteriorModeAutosomalTrisomies

Write a file with the posterior mode for each autosomal trisomy

getScaffoldsWithThisType

Getting all scaffolds classified as a specific scaffold type

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

getSamplesWithAutosomalTrisomy

Getting all samples classified as a certain autosomal trisomy

plotMCMCTrace

Plot the MCMC trace for a specific parameter

getPosteriorMeanRho

Getting posterior mean rho (ploidy ratio parameter) for each scaffold

plotTernary

Plotting the ternary of a bexy object

writePosteriorModeScaffoldTypes

Write a file with the posterior mode for each scaffold type

.getIndexScaffoldAutosomalTrisomy.bexy

Function that returns the index of a given scaffold & checks if it is valid for autosomal trisomy

bexy

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

.getInputTernary.bexy

Function that transforms state posteriors of sex karyotype to ternary-format

.getAllPossibleScaffoldTypes.bexy

Function that returns all possible scaffold types used in BeXY

.getColumns.bexy

Function to extract specific columns from a data frame or matrix

.getIndexScaffold.bexy

Function that returns the index of a given scaffold

.addLegendAutosomalTrisomy.bexy

Function to create a legend for autosomal trisomy

.plotTicTacToeWithCoordinates.bexy

Function to plot a single 7-cell plot displaying posterior probabilities of karyotypes

.getStringWidth.bexy

Function to get the width of a string on the current plotting device in user coordinates

.getScaffoldNames.bexy

Function that returns the scaffold names of z

.getSamplesToHighlight.bexy

Function to select samples that should be highlighted

.getSamplesToHighlightAutosomalTrisomy.bexy

Function to select samples that should be highlighted for autosomal trisomy

bexy (version 0.1.3)

Visualize and Parse the Output of 'BeXY'

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Functions in bexy (0.1.3)