shattered.regions: Caller for shattered genomic regions based on breakpoint...

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Description

Caller for shattered genomic regions based on breakpoint densities

Usage

shattered.regions(
  cnv,
  svc,
  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.cnv.breaks = 6,
  num.cnv.sd = 5,
  num.svc.breaks = 6,
  num.svc.sd = 5,
  num.common.breaks = 3,
  num.common.sd = 3,
  maxgap = 10000,
  chrlist = NULL,
  interleaved.cut = 0.5,
  dist.iqm.cut = 1e+05,
  verbose = TRUE
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
svc	(S4) an object of class svcnvio containing data type 'svc' validated by validate.svc
fc.pct	(numeric) inherited from cnv.breaks(); copy number change between 2 consecutive segments: i.e (default) cutoff = 0.2 represents a fold change of 0.8 or 1.2
min.cnv.size	(numeric) inherited from cnv.breaks(); The minimun segment size (in base pairs) to include in the analysis
min.num.probes	(numeric) inherited from cnv.breaks(); The minimun number of probes per segment to include in the analysis
low.cov	(data.frame) inherited from cnv.breaks(), svc.breaks() and match.breaks; a data.frame (chr, start, end) indicating low coverage regions to exclude from the analysis
clean.brk	(numeric) inherited from cnv.breaks(); n of redundant breakpoints to filter out
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.cnv.breaks	(numeric) number of segmentation breakpoints per segments to be considered high-density break
num.cnv.sd	(numeric) number of standard deviations above the sample average for num.cnv.breaks
num.svc.breaks	(numeric) number of svc breakpoints per segments to be considered high-density break
num.svc.sd	(numeric) number of standard deviations above the sample average for num.svc.breaks
num.common.breaks	(numeric) number of common SV and segmentation breakpoints per segments to be considered high-density break
num.common.sd	(numeric) number of standard deviations above the sample average for num.common.breaks
maxgap	(numeric) inherited from match.breaks(); sets the maximum gap between co-localizing orthogonal breakpoints
chrlist	(character) vector containing chromosomes to include in the analysis; if NULL all chromosomes available in the input will be included
interleaved.cut	(numeric) 0-1 value indicating percentage of interleaved (non-contiguous) SV breakpoint pairs
dist.iqm.cut	(numeric) interquantile average of the distance between breakpoints within a shattered region

Value

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

Examples

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

shattered.regions(cnv,svc)

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.