adjustA                 Adjusts alpha vector for contamination
                        karyotypes
bound                   bounds number to be in [0,1] (contamination
                        estimation)
callKaryotypes          Take prior and observed counts and calls
                        karyotypes and Z-scores
combineData             combine data
ddirichletultinomial    calculate Dirichlet probabilities with
                        filtering
dirichlet.mle_filter    calculate Dirichlet parameters with filtering
estimateGamma           Estimate contamination from XX and XY based on
                        observed counts
example_data            example_data
filterOutliers          filter for outliers
makeC                   make c vector for new karyotypes
makeDirichlet           function to make a Dirichlet prior
makeZscores             Calculates Z-scores per chromosome
plot_diagnostic         Plots diagnostic plots
printChASM              A function to print the result of the combined
                        analysis to screen
processReadCounts       processReadCounts
runChASM                Title
saveChASM               A function for saving the results of a ChASM
                        analysis as a tsv
summary_calls           summary_calls
