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cancerTiming (version 2.0.0)
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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Install
install.packages('cancerTiming')
Monthly Downloads
240
Version
2.0.0
License
GPL (>= 2)
Maintainer
Elizabeth Purdom
Last Published
May 7th, 2014
Functions in cancerTiming (2.0.0)
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mleAF
Estimate the most likely allele frequency
alleleFrequency
Get allele frequencies for tumor data
plotAlleleByPosition
plot allele frequencies by position
bootstrapEventTiming
Bootstrap the results of eventTiming
mutData
Example Mutation Data
eventTiming
Estimate the time of events in tumor data
plotSegmentation
plot segmentation(s) against positions
plotCopies
plot segmentation values against each other
makeEventHistory
Create the event history matrix
plotSeqCount
Basic function for plotting the ratio of tumor to normal coverage
multidensity
plot multiple density functions on top of each other
hg19chromosomes
Definitions of the p,q, and centromeres of chromosomes
labelSeg
Helper functions for plotting
readSimulation
Simulate reads based on an event matrix
plotAlleleDensity
plot density/histogram of allele frequencies