svc.breaks: Identify SVC breakpoints

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

Description

Transform structural varian (SVC) data.frame into a 'breaks' object

Usage

svc.breaks(svc, chrlist = NULL, low.cov = NULL)

Arguments

svc	(S4) an object of class svcnvio containing data type 'svc' initialized by validate.svc
chrlist	(character) list of chromosomes to include chr1, chr2, etc...
low.cov	(data.table) a data.table (chrom, start, end) indicating low coverage regions to exclude from the analysis

Value

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

Examples

## Obtain breakpoints from SV calls data
svc <- validate.svc(svdat_lung_ccle)

svc.breaks(svc)

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