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cancerTiming (version 3.0.0)

eventTimingOverList: eventTiming for multiple samples and regions

Description

eventTimingOverList is a wrapper to eventTiming that allows for timing of common events over several regions of a sample and/or multiple samples. getPi0Summary gets summary information about $\pi_0$ (the first event) from the output of that function and returns a simple dataframe of the estimate of $\pi_0$ for every region and sample combination.

Usage

eventTimingOverList(dfList, normCont, eventArgs)
getPi0Summary(eventList, CI = TRUE)

Arguments

dfList
a list of mutation data per sample. Each element of the list corresponds to a sample, and consists of a data frame of mutation information for all of the regions that are to be timed. The data frame must have a certain format, see description below.
normCont
a vector of equal length as dfList giving the normal contamination of each sample
eventArgs
list of arguments passed to eventTiming via `do.call'. Should NOT contain the arguments `x',`m',`history',`totalCopy',`type',`mutationId' or `normCont'
eventList
Output of eventTimingOverList (see below)
CI
logical, whether to grab CI from the output.

Value

  • eventTimingOverList returns a list equal to the number of samples. Each element of that list (i.e. per sample) is itself a list of length three corresponding to the three types of regions that can be timed, ``CNLOH",``SingleGain", and ``DoubleGain". Each of these gives the output of eventTiming per region of that type.

Details

The data frame of mutation data for each sample must have the following columns: `segId', `type', `nMutAllele', `nReads', `mutationId'. The rows of the data frame correspond to mutated locations within the sample. `segId' is an identifier of the segmented region that the mutation is in; eventTiming will be run using the mutation data for each `segId' in the sample. `type' identifies the type of segment, one of c("Other","CNLOH","SingleGain","Diploid","DoubleGain"). `nMutAllele' gives for every row (mutated location) the number of reads with the mutation and corresponds to `x' imputed into eventTiming. `nReads' gives the total number of reads covering the location and corresponds to `m' imputed into eventTiming. `mutationId' is a unique identifier for the mutation.

For arguments passed to eventTiming, it is recommended to pass verbose=FALSE if you want to avoid many warnings about mutations that do not meet the necessary criteria of coverage, etc.

See Also

eventTiming