RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (3.1.8) of this package.
Take me there.
cancerTiming (version 3.1.5)
Estimation of Temporal Ordering of Cancer Abnormalities
Description
Timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Copy Link
Copy
Link to current version
Version
Version
3.1.8
3.1.6
3.1.5
3.1.3
3.0.0
2.0.0
1.0.0
Down Chevron
Install
install.packages('cancerTiming')
Monthly Downloads
240
Version
3.1.5
License
GPL (>= 2)
Maintainer
Elizabeth Purdom
Last Published
February 9th, 2016
Functions in cancerTiming (3.1.5)
Search functions
makeEventHistory
Create the event history matrix
bootstrapEventTiming
Bootstrap the results of eventTiming
plotAlleleDensity
Plot density/histogram of allele frequencies
readSimulation
Simulate reads based on an event matrix
hg19chromosomes
Definitions of the p,q, and centromeres of chromosomes
mutData
Example Mutation Data
plotCopies
plot segmentation values against each other
eventTiming
Estimate the time of events in tumor data
plotAlleleByPosition
Plot allele frequencies by position
plotSegmentation
plot segmentation(s) against positions
multidensity
plot multiple density functions on top of each other
mut2Seg
Align mutations to segments
plotSeqCount
Basic function for plotting the ratio of tumor to normal coverage
plotPi0
Confidence intervals for $\pi_0$
alleleFrequency
Get allele frequencies for tumor data
labelSeg
Helper functions for plotting
eventTimingOverList
eventTiming for multiple samples and regions
mleAF
Estimate the most likely allele frequency