Compares sets of individuals for reccuring mutations
compareGroups(metaDataFile, outputDirectories, project, subgroups1,
subgroups2, name, includeNormal = F, clonalityCut = 0.4,
excludeSamples = c(), excludeIndividuals = c(),
cosmicDirectory = "", analysisName = "cohortAnalysis", cpus = 1,
forceRedoVariants = F, forceRedoMean = F, forceRedoMeanPlot = F,
forceRedoMatrixPlot = F, genome = "hg19", ignoreCNAonly = F,
cnvWeight = 1)character: Path to the metaData.
A named list of output directories, containing the entry Rdirectory and plotDirectory where the saved data and plots will be stored respectively.
character: The project containing the subgroups.
character: The name of the comparison. This names the output directory.
numeric: the minimum required clonality to be included in the analysis. Deafult 0.4.
character: The directory with the COSMIC data.
integer: The maximum number of parallel processes.
boolean: Force redo the mean CNAs ans SNVs rates over individuals. Default FALSE.
boolean: Force redo the mean CNA plot. Default FALSE.
boolean: Force redo the hit matrix plot. Default FALSE.
character: the genome being studied. Default "hg19".
character: The first subgroup(s).
character: The second subgroup(s).
This function runs a cohort analysis, comparing two subgroups (within a project) to each other. See cohortAnalyseBatch for details.