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cancerTiming (version 3.1.3)
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
3.1.3
License
GPL (>= 2)
Maintainer
Elizabeth Purdom
Last Published
January 4th, 2016
Functions in cancerTiming (3.1.3)
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alleleFrequency
Get allele frequencies for tumor data
labelSeg
Helper functions for plotting
multidensity
plot multiple density functions on top of each other
readSimulation
Simulate reads based on an event matrix
hg19chromosomes
Definitions of the p,q, and centromeres of chromosomes
eventTimingOverList
eventTiming for multiple samples and regions
plotSegmentation
plot segmentation(s) against positions
plotAlleleByPosition
Plot allele frequencies by position
mut2Seg
Align mutations to segments
mleAF
Estimate the most likely allele frequency
plotCopies
plot segmentation values against each other
plotSeqCount
Basic function for plotting the ratio of tumor to normal coverage
plotPi0
Confidence intervals for $\pi_0$
makeEventHistory
Create the event history matrix
bootstrapEventTiming
Bootstrap the results of eventTiming
plotAlleleDensity
Plot density/histogram of allele frequencies
mutData
Example Mutation Data
eventTiming
Estimate the time of events in tumor data