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cancerTiming (version 3.1.6)
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
install.packages('cancerTiming')
Monthly Downloads
172
Version
3.1.6
License
GPL (>= 2)
Maintainer
Elizabeth Purdom
Last Published
March 31st, 2016
Functions in cancerTiming (3.1.6)
Search functions
multidensity
plot multiple density functions on top of each other
labelSeg
Helper functions for plotting
readSimulation
Simulate reads based on an event matrix
plotAlleleByPosition
Plot allele frequencies by position
mutData
Example Mutation Data
alleleFrequency
Get allele frequencies for tumor data
hg19chromosomes
Definitions of the p,q, and centromeres of chromosomes
makeEventHistory
Create the event history matrix
eventTiming
Estimate the time of events in tumor data
plotAlleleDensity
Plot density/histogram of allele frequencies
mut2Seg
Align mutations to segments
mleAF
Estimate the most likely allele frequency
bootstrapEventTiming
Bootstrap the results of eventTiming
plotSeqCount
Basic function for plotting the ratio of tumor to normal coverage
eventTimingOverList
eventTiming for multiple samples and regions
plotCopies
plot segmentation values against each other
plotSegmentation
plot segmentation(s) against positions
plotPi0
Confidence intervals for $\pi_0$