CopywriteR (version 2.4.0)

preCopywriteR: CopywriteR: DNA copy number detection from off-target sequence data

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".

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.

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.

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)