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

118

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