Skip to contents

Filter by overlapping/non-overlapping ranges

Source: R/ranges-overlap-filter.R
ranges-filter-overlaps.Rd

Filter by overlapping/non-overlapping ranges

Usage

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

filter_by_non_overlaps(x, y, maxgap, minoverlap)

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

filter_by_non_overlaps_directed(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.

Value

a Ranges object

Details

By default, filter_by_overlaps and filter_by_non_overlaps ignore strandedness for GenomicRanges::GRanges() objects. To perform stranded operations use filter_by_overlaps_directed and filter_by_non_overlaps_directed. 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.

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)
#> GRanges object with 3 ranges and 1 metadata column:
#>       seqnames    ranges strand |        name
#>          <Rle> <IRanges>  <Rle> | <character>
#>   [1]     chr1      1-10      - |           a
#>   [2]     chr2      2-10      + |           b
#>   [3]     chr2      3-10      + |           c
#>   -------
#>   seqinfo: 4 sequences from an unspecified genome; no seqlengths

filter_by_overlaps_directed(query, subject)
#> GRanges object with 3 ranges and 1 metadata column:
#>       seqnames    ranges strand |        name
#>          <Rle> <IRanges>  <Rle> | <character>
#>   [1]     chr1      1-10      - |           a
#>   [2]     chr2      2-10      + |           b
#>   [3]     chr2      3-10      + |           c
#>   -------
#>   seqinfo: 4 sequences from an unspecified genome; no seqlengths

filter_by_non_overlaps(query, subject)
#> GRanges object with 7 ranges and 1 metadata column:
#>       seqnames    ranges strand |        name
#>          <Rle> <IRanges>  <Rle> | <character>
#>   [1]     chr3      4-10      * |           d
#>   [2]     chr3      5-10      * |           e
#>   [3]     chr3      6-10      + |           f
#>   [4]     chr4      7-10      + |           g
#>   [5]     chr4      8-10      + |           h
#>   [6]     chr4      9-10      - |           i
#>   [7]     chr4        10      - |           j
#>   -------
#>   seqinfo: 4 sequences from an unspecified genome; no seqlengths

filter_by_non_overlaps_directed(query, subject)
#> GRanges object with 7 ranges and 1 metadata column:
#>       seqnames    ranges strand |        name
#>          <Rle> <IRanges>  <Rle> | <character>
#>   [1]     chr3      4-10      * |           d
#>   [2]     chr3      5-10      * |           e
#>   [3]     chr3      6-10      + |           f
#>   [4]     chr4      7-10      + |           g
#>   [5]     chr4      8-10      + |           h
#>   [6]     chr4      9-10      - |           i
#>   [7]     chr4        10      - |           j
#>   -------
#>   seqinfo: 4 sequences from an unspecified genome; no seqlengths