cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities
Version 3.1.8

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

AuthorElizabeth Purdom
Date of publication2016-04-03 00:22:46
MaintainerElizabeth Purdom <epurdom@stat.berkeley.edu>
LicenseGPL (>= 2)
Version3.1.8
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("cancerTiming")

Popular man pages

bootstrapEventTiming: Bootstrap the results of eventTiming
hg19chromosomes: Definitions of the p,q, and centromeres of chromosomes
makeEventHistory: Create the event history matrix
mleAF: Estimate the most likely allele frequency
multidensity: plot multiple density functions on top of each other
plotAlleleByPosition: Plot allele frequencies by position
plotAlleleDensity: Plot density/histogram of allele frequencies
See all...

All man pages Function index File listing

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

Functions

allAF Man page Source code
bayesEstimate Source code
bootstrapEventTiming Man page Source code
checkLength Source code
contAF Man page Source code
decontAF Man page Source code
divideGenome Man page Source code
errorAF Man page Source code
estimateQ Source code
eventTiming Man page Source code
eventTimingOverList Man page Source code
fpath Source code
getPi0Summary Man page Source code
getPiSingle Source code
hg19chromosomes Man page
labelSeg Man page Source code
laplace Source code
logPosterior Source code
makeEventHistory Man page Source code
mleAF Man page Source code
multidensity Man page Source code
mut2Seg Man page Source code
mutData Man page
mylogSumExp Source code
numChromosome Man page Source code
parametricSimulation Source code
plotAlleleByPosition Man page Source code
plotAlleleDensity Man page Source code
plotCopies Man page Source code
plotPi0 Man page Source code
plotSegmentation Man page Source code
plotSeqCount Man page Source code
readSimulation Man page Source code
rejectsampling Source code
sir Source code

Files

inst
inst/NEWS.Rd
inst/extdata
inst/extdata/hg19chromosomes.rdata
inst/extdata/hg19chromosomes.txt
NAMESPACE
data
data/mutData.rdata
R
R/makeEventHistory.R
R/bootstrapEventTiming.R
R/eventTimingList.R
R/plotPi0.R
R/plottingCode.R
R/mut2seg.R
R/alleleFreq.R
R/labelSeg.R
R/eventTiming.R
MD5
DESCRIPTION
man
man/eventTimingOverList.Rd
man/plotAlleleByPosition.Rd
man/mut2Seg.Rd
man/mutData.Rd
man/mleAF.Rd
man/plotAlleleDensity.Rd
man/makeEventHistory.Rd
man/alleleFreq.Rd
man/readSimulation.Rd
man/bootstrapEventTiming.Rd
man/hg19chromosomes.Rd
man/multidensity.Rd
man/plotPi0.Rd
man/plotCopies.Rd
man/labelSeg.Rd
man/plotSegmentation.Rd
man/plotSeqCount.Rd
man/eventTiming.Rd
cancerTiming documentation built on May 19, 2017, 10:35 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.