alleleFreq | 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 |
mut2Seg | Align mutations to segments |
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... |
readSimulation | Simulate reads based on an event matrix |
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