splitFarNeighbour: Split segments if long gaps exist between feature positions

In biomvRCNS: Copy Number study and Segmentation for multivariate biological data

Description

Split segments if long gaps exist between feature positions, due to low coverage or resolution.

Usage

splitFarNeighbour(intStart = NULL, intEnd = NULL, xPos = NULL, xRange = NULL, maxgap = Inf, minrun = 1)

Arguments

intStart	indices of start for each segment
intEnd	indices of end for each segment
xPos	position vector, the distance of neighbouring features will be counted as point to point
xRange	IRanges / GRanges object for the positions, the the distance of neighbouring features will be counted as end to start.
maxgap	maximum distance between neighbouring features
minrun	when splitting, the minimum length of the features spanning, which half will be ignored if shorter.

Value

a list object containing the start and end indices for new segments

IS	the start indices for new segments
IE	the end indices for new segments

Author(s)

Yang Du

Examples

	set.seed(123)
	pos<-cumsum(rnbinom(20, size=10, prob=0.01))
	splitFarNeighbour(intStart=c(1, 10), intEnd=c(6, 18), xPos=pos, maxgap=1000)

biomvRCNS documentation built on Nov. 8, 2020, 6:49 p.m.