superFreq (version 1.2.3)

superCohort: 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 = "R", plotDirectory = "plots",
  cpus = 1, genome = "hg19",
  resourceDirectory = "superFreqResources", ...)

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.

cpus

integer: maximum number of threads used. default 1.

genome

character: The genome build. 'hg19', hg38' or 'mm10'. Default 'hg19'

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)

# }