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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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install.packages('cancerTiming')
Monthly Downloads
240
Version
3.1.8
License
GPL (>= 2)
Maintainer
Elizabeth Purdom
Last Published
April 2nd, 2016
Functions in cancerTiming (3.1.8)
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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