Description Usage Arguments Details Value Author(s) References Examples
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.
1 | preCopywriteR(output.folder, bin.size, ref.genome, prefix = "")
|
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". |
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.
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. |
Oscar krijgsman (o.krijgsman@nki.nl)
Thomas Kuilman (t.kuilman@nki.nl)
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.
1 2 3 4 | ## Not run:
preCopywriteR("/PATH/TO/HG19_1KB_FOLDER/", "./", 20000, "hg19")
## End(Not run)
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