Join overlaps between a query GInteractions and a GRanges
Source:R/join-overlap-left.R
ginteractions-join-overlap-left.RdJoin overlaps between a query GInteractions and a GRanges
Usage
# S3 method for class 'PinnedGInteractions'
join_overlap_left(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y"),
distance = FALSE
)
# S3 method for class 'GInteractions'
join_overlap_left(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y"),
distance = FALSE
)
# S3 method for class 'PinnedGInteractions'
join_overlap_left_directed(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y"),
distance = FALSE
)
# S3 method for class 'GInteractions'
join_overlap_left_directed(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y"),
distance = FALSE
)Arguments
- x
A (Pinned)GInteractions object
- y
A GRanges object
- maxgap, minoverlap
See
?countOverlapsin 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")).- distance
If
TRUE, add adistancecolumn: for each interaction joined to a range ofy, the distance between this range and the interaction's anchor (the pinned anchor of a PinnedGInteractions, the closer of the two anchors otherwise), as computed byGenomicRanges::distance():0when they overlap, positive when they are withinmaxgapof each other. Interactions joined to no range getNA.
Value
A GInteractions object, with the metadata columns of y (and
distance) added. Interactions overlapping several ranges of y are
repeated, and those overlapping none are kept, with missing values.
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:-")
) |> 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. Join overlaps between GInteractions and a subject GRanges
####################################################################
join_overlap_left(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
join_overlap_left_directed(gi, 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 <NA> <NA>
#> [3] gi <NA> <NA>
#> [4] gi <NA> <NA>
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. Join overlaps between PinnedGInteractions and a subject GRanges
####################################################################
gi |> pin_by("first") |> join_overlap_left(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("first") |> join_overlap_left_directed(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 <NA> <NA>
#> [2] gi <NA> <NA>
#> [3] gi <NA> <NA>
#> [4] gi <NA> <NA>
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> pin_by("second") |> join_overlap_left(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 <NA> <NA>
#> [3] gi <NA> <NA>
#> [4] gi 2 gr
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> pin_by("second") |> join_overlap_left_directed(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 <NA> <NA>
#> [3] gi <NA> <NA>
#> [4] gi <NA> <NA>
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 3. Distance between the joined ranges
####################################################################
join_overlap_left(gi, gr, maxgap = 25, distance = TRUE)
#> GInteractions object with 5 interactions and 5 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 distance
#> <character> <integer> <character> <integer>
#> [1] gi 1 gr 0
#> [2] gi 1 gr 0
#> [3] gi 1 gr 0
#> [4] gi 1 gr 0
#> [5] gi 2 gr 0
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> pin_by("second") |> join_overlap_left(gr, maxgap = 25, distance = TRUE)
#> GInteractions object with 4 interactions and 5 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 distance
#> <character> <integer> <character> <integer>
#> [1] gi 1 gr 0
#> [2] gi 1 gr 20
#> [3] gi 1 gr 20
#> [4] gi 2 gr 0
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths