Description Usage Arguments Details Value Author(s)
View source: R/fragment.genome.R
Fragment hg19 genome into consecutive bins of equal size. This function
require package BSgenome.Hsapiens.UCSC.hg19
to be installed.
1 2 3 | fragment.genome(bin.size = 1000, slid.window = bin.size,
chr.prefix = FALSE, XY.chr = FALSE, quiet = FALSE,
genome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)
|
bin.size |
the size of the bins |
slid.window |
the size of the sliding window. Default is the size of the bin, i.e. not overlapping windows. |
chr.prefix |
should chromosome name be in the form "chr1" instead of "1". Default is FALSE. |
XY.chr |
should chromosome X and Y be included. Default is FALSE. If TRUE, male and female should be analyzed separately, at least for chromosomes X and Y. |
quiet |
should any verbose display be avoided ? Default is FALSE. |
genome |
the BSgenome object with the genome. Usually BSgenome.Hsapiens.UCSC.hg19 or BSgenome.Hsapiens.UCSC.hg38. |
This requires a BSgenome, usually either hg19 or hg38. It can be install with 'source("http://bioconductor.org/biocLite.R")' and then either 'biocLite("BSgenome.Hsapiens.UCSC.hg19")' or 'biocLite("BSgenome.Hsapiens.UCSC.hg38")'.
a data.frame with columns 'chr', 'start' and 'end'.
Jean Monlong
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