fragment.genome.hg19: Fragment hg19 genome

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

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

Usage

fragment.genome.hg19(bin.size = 1000, slid.window = bin.size,
  chr.prefix = FALSE, XY.chr = FALSE, quiet = FALSE)

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.

Value

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

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.