joinRegions {regioneR} | R Documentation

## 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.

### 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)

[Package regioneR version 1.18.1 Index]