plotCNA: CopywriteR_CustomBed: ENhanced COpy number Detection from...

In PeeperLab/CopywriteRCustomBed: Copy number information from ChIP_seq using off-target reads off-target reads

Description

plotCNA analyses CopywriteR output using the segmentation algorithm CBS and creates both whole-genome and per-chromosome plots.

Usage

plotCNA(destination.folder, smoothed = TRUE, sample.plot, y.min, y.max, ...)

Arguments

destination.folder	the path to the output folder of CopywriteR_CustomBed.
smoothed	logical that determines whether DNAcopy smoothens copy number information before segmentation. Defaults to TRUE.
sample.plot	optional; a data.frame or matrix that contains the locations of sample and control BAM files. The column names should be "samples" and "controls", respectively. The file locations in a row represent a sample and its corresponding control, which is used for plotting of relative copy number values. Every sample is plotted both without a reference and with a reference. Defaults to sample.controls as used for running CopywriteR.
y.min	determines lower boundary of the plotting range.
y.max	determines upper boundary of the plotting range.
...	takes additional arguments that will be passed on to DNAcopy.

Value

segment.Rdata	an R object of the DNAcopy class, which contains the segmentation values for all analysed samples.
plots	a folder that contains all copy number profiles in portable document file (pdf) file format. Both profiles per chromosome, as well as a genome-wide profile are provided for every sample.

Author(s)

Thomas Kuilman ([e-mail])

References

CopywriteR: DNA copy number detection from off-target sequence data. Thomas Kuilman, Arno Velds, Kristel Kemper, Marco Ranzani, Lorenzo Bombardelli, Marlous Hoogstraat, Ekaterina Nevedomskaya, Guotai Xu, Julian de Ruiter, Martijn P. Lolkema, Bauke Ylstra, Jos Jonkers, Sven Rottenberg, Lodewyk F. Wessels, David J. Adams, Daniel S. Peeper, Oscar Krijgsman. Submitted for publication.

See Also

CopywriteR()

Examples

## Not run: 
setwd("/PATH/TO/BAMFILES/")
samples <- list.files(pattern = ".bam$", full.names = TRUE)
## Use the first .bam file as a reference for plotting every sample
controls <- samples[rep(1, length(samples))]
sample.plot <- data.frame(samples, controls)

plotCNA("./PATH/TO/DESTINATIONFOLDER/", sample.plot = sample.plot, y.min = -3,
        y.max = 3)

## End(Not run)

PeeperLab/CopywriteRCustomBed documentation built on May 17, 2019, 6:34 p.m.