Estimation of Temporal Ordering of Cancer Abnormalities

Documentation for package ‘cancerTiming’ version 3.1.8

allAF	Get allele frequencies for tumor data
bootstrapEventTiming	Bootstrap the results of eventTiming
contAF	Get allele frequencies for tumor data
decontAF	Get allele frequencies for tumor data
divideGenome	Helper functions for plotting
errorAF	Get allele frequencies for tumor data
eventTiming	Estimate the time of events in tumor data
eventTimingOverList	eventTiming for multiple samples and regions
getPi0Summary	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
numChromosome	Helper functions for plotting
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