superCohort: looks for reccuring events across all individuals in a batch...

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

looks for reccuring events across all individuals in a batch run

Description

looks for reccuring events across all individuals in a batch run

Usage

superCohort(
  metaDataFile,
  Rdirectory,
  plotDirectory,
  genome,
  cpus = 1,
  resourceDirectory = "superFreqResources",
  excludeIndividuals = c(),
  excludeSamples = c(),
  ...
)

Arguments

metaDataFile	character: path to the tab separated meta data file.
Rdirectory	character: path to the Rdirectory of the batch run.
plotDirectory	character: path to the plotDirectory of the batch run.
genome	character: The genome build. 'hg19', hg38' or 'mm10'. Default 'hg19'
cpus	integer: maximum number of threads used. default 1.
resourceDirectory	character: path to the superFreq resources. Default 'superFreqResources'.
...:	Remaing argument are passed to superFreq::cohortAnalyseBatch()

Details

This function merges the data from multiple batches, setting them up for a joint cohort analysis. Note that this is only for the purpose of a downstream cohort analysis. The output R directory cannot be run as a batch Rdirectory.

Examples

## Not run: 
superFreq(metaDataFile=metaDataFile,
          Rdirectory=Rdirectory,
          plotDirectory=plotDirectory,
          cpus=cpus,
          genome=genome)

#The resource directory defaults to the same in superFreq() and superCohort()
#so do not need to be specified.
superCohort(metaDataFile=metaDataFile,
          Rdirectory=Rdirectory,
          plotDirectory=plotDirectory,
          cpus=cpus,
          genome=genome)


## End(Not run)

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.