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cancerTiming (version 1.0.0)

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

1.0.0

License

GPL (>= 2)

Maintainer

Elizabeth Purdom

Last Published

August 29th, 2012

Functions in cancerTiming (1.0.0)

alleleFrequency

Get allele frequencies for tumor data
plotCopies

plot segmentation values against each other
eventTiming

Estimate the time of events in tumor data
hg19chromosomes

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

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

plot multiple density functions on top of each other
plotAlleleByPosition

plot allele frequencies by position
plotAlleleDensity

plot density/histogram of allele frequencies
mleAF

Estimate the most likely allele frequency
makeEventHistory

Create the event history matrix
plotSegmentation

plot segmentation(s) against positions
mutData

Example Mutation Data
bootstrapEventTiming

Bootstrap the results of eventTiming
labelSeg

Helper functions for plotting
readSimulation

Simulate reads based on an event matrix