filter_by_overlaps {plyranges} | R Documentation

## Filter by overlapping/non-overlapping ranges

### Description

Filter by overlapping/non-overlapping ranges

### Usage

    filter_by_overlaps(x, y, maxgap = -1L, minoverlap = 0L)

    filter_by_non_overlaps(x, y, maxgap, minoverlap)

### Arguments

`x, y` | Objects representing ranges
`maxgap` | The maximimum gap between intervals as a single integer greater than or equal to -1. If you modify this argument, `minoverlap` must be held fixed.
`minoverlap` | The minimum amount of overlap between intervals as a single integer greater than 0. If you modify this argument, `maxgap` must be held fixed.

### Details

By default, `filter_by_overlaps` and `filter_by_non_overlaps` ignore strandedness for `GRanges()` objects. The argument `maxgap` is the maximum number of positions between two ranges for them to be considered overlapping. Here the default is set to be -1 as that is the the gap between two ranges that has its start or end strictly inside the other. The argugment `minoverlap` refers to the minimum number of positions overlapping between ranges, to consider there to be overlap.

### Value

a Ranges object

### See Also

`IRanges::subsetByOverlaps()`

### Examples

    df <- data.frame(seqnames = c("chr1", rep("chr2", 2),
                                  rep("chr3", 3), rep("chr4", 4)),
                     start = 1:10,
                     width = 10:1,
                     strand = c("-", "+", "+", "*", "*", "+", "+", "+", "-", "-"),
                     name = letters[1:10])
    query <- as_granges(df)

    df2 <- data.frame(seqnames = c(rep("chr2", 2), rep("chr1", 3), "chr2"),
                      start = c(4,3,7,13,1,4),
                      width = c(6,6,3,3,3,9),
                      strand = c(rep("+", 3), rep("-", 3)))
    subject <- as_granges(df2)

    filter_by_overlaps(query, subject)

    filter_by_non_overlaps(query, subject)

[Package plyranges version 1.12.1 Index]