preCopywriteR: CopywriteR_ChIP: DNA copy number detection from off-target...

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

Description

preCopywriteR is used to generate helper files (blacklist, bin region, GC-content, and mappability .bed files) for the desired bin size from pre-assembled 1 kb helper files. These binary 1 kb helper files are available at https://github.com/PeeperLab/CopywriteR for hg18, hg19, hg38, mm9 and mm10 reference genomes.

Usage

preCopywriteR(output.folder, bin.size, ref.genome, prefix = "")

Arguments

output.folder	the path to the output folder.
bin.size	desired bin length (in bp) for which helper files should be generated.
ref.genome	the reference genome for which helper files should be generated, e.g. hg18, hg19, hg38, mm9 or mm10.
prefix	the prefix that is used for chromosome notation. Standard notation is "1", "2", ..., "X", "Y". For "chr1", ... notation, use prefix = "chr".

Details

Currently helper files can be generated for human (hg18, hg19 and hg38) and mouse (mm9 and mm10) reference genomes.

Helper files can only be generated for a bin.size that is a multiple of 1000 bp.

Value

blacklist.rda	an R data file containing a GRanges object with blacklisted regions of known CNVs.
GC_mappability.rda	an R data file containing a GRanges object with the mappability and GC-content for bins of the specified size.

Author(s)

Oscar krijgsman ([e-mail])
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.

Examples

## Not run: 
preCopywriteR("/PATH/TO/HG19_1KB_FOLDER/", "./", 20000, "hg19")

## End(Not run)

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