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

Description Usage Arguments Value Examples

View source: R/shattered.regions.r

Description

Caller for shattered genomic regions based on breakpoint densities

Usage

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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

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

shattered.regions(cnv,svc)

gonzolgarcia/svpluscnv documentation built on March 4, 2020, 10:06 a.m.