ssvConsensusIntervalSets {seqsetvis} | R Documentation

## Intersect a list of GRanges to create a single GRanges object of merged ranges including metadata describing overlaps per input GRanges.

### Description

In constrast to ssvOverlapIntervalSets, only regions where a consensus of input grs are present are preserved and annotated.

### Usage

    ssvConsensusIntervalSets(grs, ext = 0, min_number = 2, min_fraction = 0.5, ...)

### Arguments

`grs` | A list of GRanges
`ext` | An integer specifying how far to extend ranges before merging. in effect, ranges withing 2*ext of one another will be joined during the merge
`min_number` | An integer number specifying the absloute minimum of input grs that must overlap for a site to be considered consensus.
`min_fraction` | A numeric between 0 and 1 specifying the fraction of grs that must overlap to be considered consensus.
`...` | arguments passed to IRanges::findOverlaps, i.e. maxgap, minoverlap, type, select, invert.

### Details

Only the most stringent of min_number or min_fraction will be applied.

### Value

GRanges with metadata columns describing consensus overlap of input grs.

### Examples

    library(GenomicRanges)
    a = GRanges("chr1", IRanges(1:7*10, 1:7*10))
    b = GRanges("chr1", IRanges(5:10*10, 5:10*10))
    ssvConsensusIntervalSets(list(a, b))

[Package seqsetvis version 1.10.0 Index]