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 |

**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

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

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