compareGroups: Compares sets of individuals for reccuring mutations

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

Compares sets of individuals for reccuring mutations

Description

Compares sets of individuals for reccuring mutations

Usage

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
)

Arguments

metaDataFile	character: Path to the metaData.
outputDirectories	A named list of output directories, containing the entry Rdirectory and plotDirectory where the saved data and plots will be stored respectively.
project	character: The project containing the subgroups.
name	character: The name of the comparison. This names the output directory.
clonalityCut	numeric: the minimum required clonality to be included in the analysis. Deafult 0.4.
cosmicDirectory	character: The directory with the COSMIC data.
cpus	integer: The maximum number of parallel processes.
forceRedoMean	boolean: Force redo the mean CNAs ans SNVs rates over individuals. Default FALSE.
forceRedoMeanPlot	boolean: Force redo the mean CNA plot. Default FALSE.
forceRedoMatrixPlot	boolean: Force redo the hit matrix plot. Default FALSE.
genome	character: the genome being studied. Default "hg19".
subgroup1	character: The first subgroup(s).
subgroup2	character: The second subgroup(s).

Details

This function runs a cohort analysis, comparing two subgroups (within a project) to each other. See cohortAnalyseBatch for details.

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