match.breaks: Compare two different sets of breakpoints

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

Description

Compare two different sets of breakpoints

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' or 'cnv.breaks'
brk2	(S4) an object of class breaks as returned by 'svc.breaks' or 'cnv.breaks' to compare against brk1
maxgap	(numeric) distance (base pairs) limit for breakpoints to be considered colocalized
verbose	(logical)

Value

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

Examples

## Obtain breakpoints from segmentation data
cnv <- validate.cnv(segdat_lung_ccle)
brk1 <- cnv.breaks(cnv)

## Obtain breakpoints from SV calls data
sv <- validate.svc(svdat_lung_ccle)
brk2 <- svc.breaks(svc)

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

## average percentage of colocalizing breaks
restab <- data.frame(common.breaks$restab)[order(common.breaks$restab$total.brk2),]
m2 <- sprintf("%.1f",100*mean(restab$matched.brk2/restab$total.brk2)) 

## Plot the proportion of SV breakpoints that have colocalizing CNV breakpoints
barplot(rbind(restab$matched.brk2, restab$total.brk2 - restab$matched.brk2),
        border=NA,las=2,xlab="",horiz=FALSE,cex.main=.7,cex.names=.4, names=rownames(restab))
legend("top",paste("SV breaks matched by CNV breaks\n","Average = ",m2,"%",sep=""),bty='n')
grid(ny=NULL,nx=NA)

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