fragment.genome: Fragment a genome

Description Usage Arguments Details Value Author(s)

View source: R/fragment.genome.R

Description

Fragment hg19 genome into consecutive bins of equal size. This function require package BSgenome.Hsapiens.UCSC.hg19 to be installed.

Usage

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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)

Arguments

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.

Details

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")'.

Value

a data.frame with columns 'chr', 'start' and 'end'.

Author(s)

Jean Monlong


jmonlong/PopSV documentation built on July 1, 2018, 10:14 p.m.