mergeRegions: Merge Regions

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

Merge Regions

Description

Merges the overlapping regions from two region sets. The two region sets are first merged into one and then overlapping regions are fused.

Usage

mergeRegions(A, B)

Arguments

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

Value

It returns a GenomicRanges object with the regions resulting from the merging process. Any two overlapping regions from any of the two sets will be fused into one.

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, joinRegions, commonRegions, overlapRegions

Examples

A <- data.frame("chr1", c(1, 5, 20, 30), c(8, 13, 28, 40), x=c(1,2,3,4), y=c("a", "b", "c", "d"))

B <- data.frame("chr1", 25, 35)

merges <- mergeRegions(A, B)

plotRegions(list(A, B, merges), chromosome="chr1", regions.labels=c("A", "B", "merges"), regions.colors=3:1)

bernatgel/regioneR documentation built on Sept. 10, 2023, 12:03 a.m.