regioneR (version 1.4.0)

joinRegions: Join Regions

Description

Joins the regions from a region set A that are less than min.dist bases apart.

Usage

joinRegions(A, min.dist=1)

Arguments

A

a region set in any of the accepted formats by toGRanges (GenomicRanges, data.frame, etc...)

min.dist

an integer indicating the minimum distance required between two regions in order to not fuse them. Any pair of regions closer than min.dist bases will be fused in a larger region. Defaults to 1, so it will only join overlapping regions.

Value

It returns a GenomicRanges object with the regions resulting from the joining process.

See Also

plotRegions, toDataframe, toGRanges, subtractRegions, splitRegions, extendRegions, commonRegions, mergeRegions, overlapRegions

Examples

A <- data.frame("chr1", c(1, 10, 20, 30), c(12, 13, 28, 40))

join1 <- joinRegions(A)

join2 <- joinRegions(A, min.dist=3)

join3 <- joinRegions(A, min.dist=10)

plotRegions(list(A, join1, join2, join3), chromosome="chr1", regions.labels=c("A", "join1", "join2", "join3"), regions.colors=4:1)