cohortAnalyseBatch: Analyse individuals for reccuring mutations

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

Analyse individuals for reccuring mutations

Description

Analyse individuals for reccuring mutations

Usage

cohortAnalyseBatch(
  metaDataFile,
  outputDirectories,
  cpus = 1,
  onlyDNA = T,
  clonalityCut = 0.4,
  includeNormal = F,
  excludeSamples = c(),
  excludeIndividuals = c(),
  cosmicDirectory = "",
  analysisName = "cohortAnalysis",
  cnvWeight = 1,
  forceRedoVariants = F,
  forceRedoMean = F,
  forceRedoMatrixPlot = F,
  forceRedoMeanPlot = F,
  genome = "hg19",
  ignoreCNAonly = F
)

Arguments

metaDataFile	character: path to the metaData file.
outputDirectories	A named list of output directories, containing the entries Rdirectory and plotDirectory where the saved data and plots will be stored respectively.
cpus	integer: the maximum number of cpus to run on.
clonalityCut	numeric: the minimum required clonality to be included in the analysis. Deafult 0.4.
excludeSamples	character: The samples to be excluded from the analysis. Default c().
excludeIndividuals	character: The individuals to be excluded from the analysis. Default c().
cosmicDirectory	character: The directory with the COSMIC data.
analysisName	character: The name of the directory where the analysis results are saved. Default "cohortAnalysis".
forceRedoVariants	boolean: Force redo the merging of the variants between individuals. Default FALSE.
forceRedoMean	boolean: Force redo the mean CNAs ans SNVs rates over individuals. Default FALSE.
forceRedoMatrixPlot	boolean: Force redo the hit matrix plot. Default FALSE.
forceRedoMeanPlot	boolean: Force redo the mean CNA plot. Default FALSE.
genome	character: the genome being studied. Default "hg19".

Details

This function calculates mutation rates over genes, both protein changing SNVs, as well as CNA rates for complete loss, loss, gain (3 copies) and amplification (4 or more copies). It also track biallelic loss of genes in samples, by complete loss, a protein changing SNV plus a loss, or two SNVs (that are assumed to be on different alleles). Output is a plot over the genome of the CNA rates, as well as a "top table" of frequently mutated genes. It is run as an afterburner, and needs a finished superFreq analysis to be run on the samples.

Examples

## Not run: 
metaDataFile = '/absolute/path/to/metaData.txt'

Rdirectory = '/absolute/path/to/R'
plotDirectory = '/absolute/path/to/plots'

cpus=6
genome = 'hg19'

outputDirectories = list('Rdirectory'=Rdirectory, 'plotDirectory'=plotDirectory)

cohortAnalyseBatch(metaDataFile, outputDirectories, cpus=cpus, genome=genome)


## End(Not run)

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