cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

Timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.

Author
Elizabeth Purdom
Date of publication
2016-04-03 00:22:46
Maintainer
Elizabeth Purdom <epurdom@stat.berkeley.edu>
License
GPL (>= 2)
Version
3.1.8

View on CRAN

Man pages

alleleFreq
Get allele frequencies for tumor data
bootstrapEventTiming
Bootstrap the results of eventTiming
eventTiming
Estimate the time of events in tumor data
eventTimingOverList
eventTiming for multiple samples and regions
hg19chromosomes
Definitions of the p,q, and centromeres of chromosomes
labelSeg
Helper functions for plotting
makeEventHistory
Create the event history matrix
mleAF
Estimate the most likely allele frequency
multidensity
plot multiple density functions on top of each other
mut2Seg
Align mutations to segments
mutData
Example Mutation Data
plotAlleleByPosition
Plot allele frequencies by position
plotAlleleDensity
Plot density/histogram of allele frequencies
plotCopies
plot segmentation values against each other
plotPi0
Confidence intervals for pi[0]
plotSegmentation
plot segmentation(s) against positions
plotSeqCount
Basic function for plotting the ratio of tumor to normal...
readSimulation
Simulate reads based on an event matrix

Files in this package

cancerTiming
cancerTiming/inst
cancerTiming/inst/NEWS.Rd
cancerTiming/inst/extdata
cancerTiming/inst/extdata/hg19chromosomes.rdata
cancerTiming/inst/extdata/hg19chromosomes.txt
cancerTiming/NAMESPACE
cancerTiming/data
cancerTiming/data/mutData.rdata
cancerTiming/R
cancerTiming/R/makeEventHistory.R
cancerTiming/R/bootstrapEventTiming.R
cancerTiming/R/eventTimingList.R
cancerTiming/R/plotPi0.R
cancerTiming/R/plottingCode.R
cancerTiming/R/mut2seg.R
cancerTiming/R/alleleFreq.R
cancerTiming/R/labelSeg.R
cancerTiming/R/eventTiming.R
cancerTiming/MD5
cancerTiming/DESCRIPTION
cancerTiming/man
cancerTiming/man/eventTimingOverList.Rd
cancerTiming/man/plotAlleleByPosition.Rd
cancerTiming/man/mut2Seg.Rd
cancerTiming/man/mutData.Rd
cancerTiming/man/mleAF.Rd
cancerTiming/man/plotAlleleDensity.Rd
cancerTiming/man/makeEventHistory.Rd
cancerTiming/man/alleleFreq.Rd
cancerTiming/man/readSimulation.Rd
cancerTiming/man/bootstrapEventTiming.Rd
cancerTiming/man/hg19chromosomes.Rd
cancerTiming/man/multidensity.Rd
cancerTiming/man/plotPi0.Rd
cancerTiming/man/plotCopies.Rd
cancerTiming/man/labelSeg.Rd
cancerTiming/man/plotSegmentation.Rd
cancerTiming/man/plotSeqCount.Rd
cancerTiming/man/eventTiming.Rd