shattered.regions.cnv: CNV-only based shattered region detection

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Caller for the identification of shattered genomic regions based on CNV breakpoint densities

Usage

shattered.regions.cnv(
  cnv,
  fc.pct = 0.2,
  min.cnv.size = 0,
  min.num.probes = 0,
  low.cov = NULL,
  clean.brk = NULL,
  window.size = 10,
  slide.size = 2,
  num.breaks = 10,
  num.sd = 5,
  dist.iqm.cut = 1e+05,
  chrlist = NULL,
  chr.lim = NULL,
  verbose = TRUE
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' initialized by validate.cnv
fc.pct	(numeric) copy number change between 2 consecutive segments: i.e (default) cutoff = 0.2 represents 20 percent fold change
min.cnv.size	(numeric) The minimun segment size (in base pairs) to include in the analysis
min.num.probes	(numeric) The minimun number of probes per segment to include in the analysis
low.cov	(data.frame) a data.frame (chr, start, end) indicating low coverage regions to exclude from the analysis
clean.brk	(numeric) inherited from cnv.breaks(); n cutoff for redundant breakpoints to filter out; if NULL, no filter will be applied
window.size	(numeric) size in megabases of the genmome bin to compute break density
slide.size	(numeric) size in megabases of the sliding genmome window
num.breaks	(numeric) size in megabases of the genmome bin to compute break density
num.sd	(numeric) size in megabases of the sliding genmome window
dist.iqm.cut	(numeric) interquantile average of the distance between breakpoints within a shattered region
chrlist	(character) vector containing chromosomes to include in the analysis; if NULL all chromosomes available in the input will be included
verbose	(logical)

Value

an instance of the class 'chromo.regs' containing breakpoint mapping onto genes

Examples

## validate input data.frames
cnv <- validate.cnv(segdat_lung_ccle)

shattered.regions.cnv(cnv)

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.