cnv.breaks: Identify CNV breakpoints filtered by the change in copy...

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

Description

Identify CNV breakpoints filtered by the change in copy number logRs between contiguous segments

Usage

cnv.breaks(
  cnv,
  fc.pct = 0.2,
  break.width = 10000,
  min.cnv.size = NULL,
  min.num.probes = NULL,
  chrlist = NULL,
  low.cov = NULL,
  clean.brk = NULL,
  verbose = TRUE
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
fc.pct	(numeric) copy number change between 2 consecutive segments: i.e (default) cutoff = 0.2 represents a fold change of 0.8 or 1.2
break.width	(numeric) the maximum distance between a segment end and the subsequent segment start positions beyond which breakpoints are discarded
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) identical breakpoints across multiple samples tend to be artifacts; remove breaks > N

Value

an instance of the class 'breaks' containing breakpoint and breakpoint burden information

Examples

## Obtain breakpoints from segmentation data
cnv <- validate.cnv(segdat_lung_ccle)

cnv.breaks(cnv)

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