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cancerTiming (version 3.1.8)

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')

Monthly Downloads

93

Version

3.1.8

License

GPL (>= 2)

Maintainer

Elizabeth Purdom

Last Published

April 2nd, 2016

Functions in cancerTiming (3.1.8)

hg19chromosomes

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

Create the event history matrix
plotAlleleDensity

Plot density/histogram of allele frequencies
eventTiming

Estimate the time of events in tumor data
alleleFrequency

Get allele frequencies for tumor data
mleAF

Estimate the most likely allele frequency
plotSegmentation

plot segmentation(s) against positions
plotCopies

plot segmentation values against each other
mut2Seg

Align mutations to segments
eventTimingOverList

eventTiming for multiple samples and regions
mutData

Example Mutation Data
labelSeg

Helper functions for plotting
multidensity

plot multiple density functions on top of each other
plotAlleleByPosition

Plot allele frequencies by position
plotPi0

Confidence intervals for $pi[0]$
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