match.breaks: Breakpoint matching

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

Description

Match common breakpoints from two different datasets or data types based on their co-localization in the genome.

Usage

match.breaks(brk1, brk2, maxgap = 1e+05, verbose = FALSE, plot = TRUE)

Arguments

brk1	(S4) an object of class breaks as returned by 'svc.breaks' and 'cnv.breaks'
brk2	(S4) an object of class breaks as returned by 'svc.breaks' and 'cnv.breaks' to compare against brk1
maxgap	(numeric) distance (base pairs) limit for nreakpoints to be consider colocalized
verbose	(logical) whether to return internal messages
plot	(logical) whether to plot into open device

Value

an object containing co-localizing breakpoints from two input 'breaks'

Examples

# initialize CNV and SVC data
cnv <- validate.cnv(segdat_lung_ccle)
svc <- validate.svc(svdat_lung_ccle)

## Obtain breakpoints from CNV and SVC
brk1 <- cnv.breaks(cnv)
brk2 <- svc.breaks(svc)

common.brk <- match.breaks(brk1, brk2)

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