runDE: Run differential coverage analysis.

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

Run differential coverage analysis.

Description

Run differential coverage analysis.

Usage

runDE(
  bamFiles,
  sampleNames,
  externalNormalBams,
  captureRegions,
  Rdirectory,
  plotDirectory,
  normalRdirectory,
  settings = list(),
  genome = "hg19",
  cpus = 1,
  mode = "exome",
  forceRedoFit = F,
  forceRedoCount = F,
  forceRedoNormalCount = F,
  isPairedEnd = TRUE,
  countReadPairs = TRUE
)

Arguments

bamFiles	vector of paths to the bamfiles to be analysed
sampleNames	vector of names of the samples associated with the bam files.
externalNormalBams	vector of paths to the pool of normal samples.
captureRegions	GRanges capture regions, as you get from importCaptureRegions.
Rdirectory	The directory to save or load the output to/from.
plotDirectory	The directory to plot results and diagnosis to.
normalRdirectory	The directory to save or load the pool of normal counts to/from.
settings	Settings as passed to analyse(...).
genome	Character string of the genome, such as 'hg19', 'hg38' or 'mm10'. Defaults to 'hg19'.
cpus	The number of parallel cpus to be used. Defaults to 1.
forceRedoFit	Boolean, forcing the differential analysis to be redone even if saved data is present. Defaults to FALSE.
forceRedoCount	Boolean, forcing the counting to be redone even if saved data is present. Defaults to FALSE.
forceRedoNormalCount	Boolean, forcing the counting of normal samples to be redone even if saved data is present. Defaults to FALSE.

Details

Reads in the bed file into GRanges format, with extra columns for GC and binding strength.

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