allAF                   Get allele frequencies for tumor data
bootstrapEventTiming    Bootstrap the results of eventTiming
eventTiming             Estimate the time of events in tumor data
eventTimingOverList     eventTiming for multiple samples and regions
hg19chromosomes         Definitions of the p,q, and centromeres of
                        chromosomes
labelSeg                Helper functions for plotting
makeEventHistory        Create the event history matrix
mleAF                   Estimate the most likely allele frequency
multidensity            plot multiple density functions on top of each
                        other
mutData                 Example Mutation Data
plotAlleleByPosition    Plot allele frequencies by position
plotAlleleDensity       Plot density/histogram of allele frequencies
plotCopies              plot segmentation values against each other
plotPi0                 Confidence intervals for pi[0]
plotSegmentation        plot segmentation(s) against positions
plotSeqCount            Basic function for plotting the ratio of tumor
                        to normal coverage
readSimulation          Simulate reads based on an event matrix
