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cancerTiming (version 3.0.0)

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')

Monthly Downloads

62

Version

3.0.0

License

GPL (>= 2)

Maintainer

Elizabeth Purdom

Last Published

April 13th, 2015

Functions in cancerTiming (3.0.0)

bootstrapEventTiming

Bootstrap the results of eventTiming
plotSeqCount

Basic function for plotting the ratio of tumor to normal coverage
readSimulation

Simulate reads based on an event matrix
eventTimingOverList

eventTiming for multiple samples and regions
plotAlleleByPosition

Plot allele frequencies by position
plotPi0

Confidence intervals for $\pi_0$
plotSegmentation

plot segmentation(s) against positions
makeEventHistory

Create the event history matrix
labelSeg

Helper functions for plotting
mleAF

Estimate the most likely allele frequency
plotAlleleDensity

Plot density/histogram of allele frequencies
eventTiming

Estimate the time of events in tumor data
alleleFrequency

Get allele frequencies for tumor data
plotCopies

plot segmentation values against each other
hg19chromosomes

Definitions of the p,q, and centromeres of chromosomes
mutData

Example Mutation Data
multidensity

plot multiple density functions on top of each other