Run differential coverage analysis.
runDE(bamFiles, names, externalNormalBams, captureRegions, Rdirectory,
plotDirectory, normalRdirectory, settings = list(), genome = "hg19",
cpus = 1, mode = "exome", forceRedoFit = F, forceRedoCount = F,
forceRedoNormalCount = F)vector of paths to the bamfiles to be analysed
vector of names of the samples associated with the bam files.
vector of paths to the pool of normal samples.
GRanges capture regions, as you get from importCaptureRegions.
The directory to save or load the output to/from.
The directory to plot results and diagnosis to.
The directory to save or load the pool of normal counts to/from.
Settings as passed to analyse(...).
Character string of the genome, such as 'hg19', 'hg38' or 'mm10'. Defaults to 'hg19'.
The number of parallel cpus to be used. Defaults to 1.
Boolean, forcing the differential analysis to be redone even if saved data is present. Defaults to FALSE.
Boolean, forcing the counting to be redone even if saved data is present. Defaults to FALSE.
Boolean, forcing the counting of normal samples to be redone even if saved data is present. Defaults to FALSE.
Reads in the bed file into GRanges format, with extra columns for GC and binding strength.