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cancerTiming (version 3.1.3)

Estimation of Temporal Ordering of Cancer Abnormalities

Description

This is a package with functions for 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

3.1.3

License

GPL (>= 2)

Maintainer

Elizabeth Purdom

Last Published

January 4th, 2016

Functions in cancerTiming (3.1.3)

alleleFrequency

Get allele frequencies for tumor data

labelSeg

Helper functions for plotting

multidensity

plot multiple density functions on top of each other

readSimulation

Simulate reads based on an event matrix

hg19chromosomes

Definitions of the p,q, and centromeres of chromosomes

eventTimingOverList

eventTiming for multiple samples and regions

plotSegmentation

plot segmentation(s) against positions

plotAlleleByPosition

Plot allele frequencies by position

mut2Seg

Align mutations to segments

mleAF

Estimate the most likely allele frequency

plotCopies

plot segmentation values against each other

plotSeqCount

Basic function for plotting the ratio of tumor to normal coverage

plotPi0

Confidence intervals for $\pi_0$

makeEventHistory

Create the event history matrix

bootstrapEventTiming

Bootstrap the results of eventTiming

plotAlleleDensity

Plot density/histogram of allele frequencies

mutData

Example Mutation Data

eventTiming

Estimate the time of events in tumor data