Find overlaps between a query GInteractions and a GRanges
Source:R/find-overlaps.R
ginteractions-find-overlaps.RdFind overlaps between a query GInteractions and a GRanges
Usage
# S3 method for class 'PinnedGInteractions'
find_overlaps(x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y"))
# S3 method for class 'GInteractions'
find_overlaps(x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y"))
# S3 method for class 'PinnedGInteractions'
find_overlaps_directed(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y")
)
# S3 method for class 'GInteractions'
find_overlaps_directed(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y")
)Arguments
- x
A (Pinned)GInteractions object
- y
A GRanges object
- maxgap, minoverlap
See
?findOverlapsin the GenomicRanges package for a description of these arguments- suffix
Suffix to add to metadata columns (character vector of length 2, default to
c(".x", ".y")).
Rationale
find_overlaps() will search for any overlap between GInteractions
in x and GRanges in y. It will return a GInteractions
object of length equal to the number of times x overlaps y.
This GInteractions will have additional metadata columns
corresponding to the metadata from y. find_overlaps_directed()
takes the strandness of each object into account.
Pinned GInteractions
When using find_overlaps() with a PinnedGInteractions object,
only the pinned anchors are used to check for overlap with y.
This is equivalent to specifying use.region="both" in
InteractionSet::findOverlaps().
Examples
gi <- read.table(text = "
chr1 11 20 - chr1 21 30 +
chr1 11 20 - chr1 51 55 +
chr1 21 30 - chr1 51 55 +
chr1 21 30 - chr2 51 60 +",
col.names = c(
"seqnames1", "start1", "end1", "strand1",
"seqnames2", "start2", "end2", "strand2"
)
) |> as_ginteractions() |> mutate(id = 1:4, type = 'gi')
gr <- GenomicRanges::GRanges(
c("chr1:20-30:+", "chr2:55-65:-")
) |> plyranges::mutate(id = 1:2, type = 'gr')
gi
#> GInteractions object with 4 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | 1
#> [2] chr1 11-20 - --- chr1 51-55 + | 2
#> [3] chr1 21-30 - --- chr1 51-55 + | 3
#> [4] chr1 21-30 - --- chr2 51-60 + | 4
#> type
#> <character>
#> [1] gi
#> [2] gi
#> [3] gi
#> [4] gi
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gr
#> GRanges object with 2 ranges and 2 metadata columns:
#> seqnames ranges strand | id type
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] chr1 20-30 + | 1 gr
#> [2] chr2 55-65 - | 2 gr
#> -------
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 1. Find overlaps between GInteractions and a subject GRanges
####################################################################
find_overlaps(gi, gr)
#> GInteractions object with 5 interactions and 4 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.x
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | 1
#> [2] chr1 11-20 - --- chr1 51-55 + | 2
#> [3] chr1 21-30 - --- chr1 51-55 + | 3
#> [4] chr1 21-30 - --- chr2 51-60 + | 4
#> [5] chr1 21-30 - --- chr2 51-60 + | 4
#> type.x id.y type.y
#> <character> <integer> <character>
#> [1] gi 1 gr
#> [2] gi 1 gr
#> [3] gi 1 gr
#> [4] gi 1 gr
#> [5] gi 2 gr
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
find_overlaps_directed(gi, gr)
#> GInteractions object with 1 interaction and 4 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.x
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | 1
#> type.x id.y type.y
#> <character> <integer> <character>
#> [1] gi 1 gr
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. Find overlaps between PinnedGInteractions and a subject GRanges
####################################################################
gi |> pin_by("first") |> find_overlaps(gr)
#> GInteractions object with 4 interactions and 4 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.x
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | 1
#> [2] chr1 11-20 - --- chr1 51-55 + | 2
#> [3] chr1 21-30 - --- chr1 51-55 + | 3
#> [4] chr1 21-30 - --- chr2 51-60 + | 4
#> type.x id.y type.y
#> <character> <integer> <character>
#> [1] gi 1 gr
#> [2] gi 1 gr
#> [3] gi 1 gr
#> [4] gi 1 gr
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> pin_by("second") |> find_overlaps(gr)
#> GInteractions object with 2 interactions and 4 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.x
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | 1
#> [2] chr1 21-30 - --- chr2 51-60 + | 4
#> type.x id.y type.y
#> <character> <integer> <character>
#> [1] gi 1 gr
#> [2] gi 2 gr
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> pin_by("first") |> find_overlaps_directed(gr)
#> GInteractions object with 0 interactions and 4 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.x
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> type.x id.y type.y
#> <character> <integer> <character>
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> pin_by("second") |> find_overlaps_directed(gr)
#> GInteractions object with 1 interaction and 4 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.x
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | 1
#> type.x id.y type.y
#> <character> <integer> <character>
#> [1] gi 1 gr
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths