joinRegions: Join Regions

In regioneR: Association analysis of genomic regions based on permutation tests

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.

Note

All metadata (additional columns in the region set in addition to chromosome, start and end) will be ignored and not present in the returned region set.

The implementation relies completely in the reduce function from IRanges package.

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)

regioneR documentation built on Nov. 8, 2020, 5 p.m.