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cancerTiming (version 3.1.6)

Estimation of Temporal Ordering of Cancer Abnormalities

Description

Timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.

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Version

Install

install.packages('cancerTiming')

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Version

3.1.6

License

GPL (>= 2)

Maintainer

Elizabeth Purdom

Last Published

March 31st, 2016

Functions in cancerTiming (3.1.6)

multidensity

plot multiple density functions on top of each other

labelSeg

Helper functions for plotting

readSimulation

Simulate reads based on an event matrix

plotAlleleByPosition

Plot allele frequencies by position

mutData

Example Mutation Data

alleleFrequency

Get allele frequencies for tumor data

hg19chromosomes

Definitions of the p,q, and centromeres of chromosomes

makeEventHistory

Create the event history matrix

eventTiming

Estimate the time of events in tumor data

plotAlleleDensity

Plot density/histogram of allele frequencies

mut2Seg

Align mutations to segments

mleAF

Estimate the most likely allele frequency

bootstrapEventTiming

Bootstrap the results of eventTiming

plotSeqCount

Basic function for plotting the ratio of tumor to normal coverage

eventTimingOverList

eventTiming for multiple samples and regions

plotCopies

plot segmentation values against each other

plotSegmentation

plot segmentation(s) against positions

plotPi0

Confidence intervals for $\pi_0$