hot.spot.samples: Hot-spot sample retrieval

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

Description

Collects sample ids with shattered regions detected at hot-spots based on certain p-value cutoff

Usage

hot.spot.samples(chromo.regs.obj, freq.cut)

Arguments

chromo.regs.obj	(chromo.regs) An object of class chromo.regs
freq.cut	(numeric) the hot spot threshold above which peaks are defined for sample ID retrieval

Value

a list comprising two lists: peakRegions, peakRegionsSamples

Examples

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

chromo.regs.obj <- shattered.regions(cnv,svc)
mat<-hbd.mat(chromo.regs.obj)

pcut.obj <- freq.p.test(mat,plot=FALSE)
pcut <- freq.threshold(pcut.obj)

res <- hot.spot.samples(chromo.regs.obj,pcut)

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