Replace anchors of a GInteractions
Usage
replace_anchors(x, id, value)
# S4 method for class 'GInteractions,character,GenomicRanges'
replace_anchors(x, id, value)
# S4 method for class 'GInteractions,numeric,GenomicRanges'
replace_anchors(x, id, value)
# S4 method for class 'PinnedGInteractions,missing,GenomicRanges'
replace_anchors(x, id, value)
# S4 method for class 'AnchoredPinnedGInteractions,missing,GRanges'
replace_anchors(x, id, value)
# S4 method for class 'AnchoredPinnedGInteractions,numeric,GRanges'
replace_anchors(x, id, value)Examples
gi <- read.table(text = "
chr1 11 20 chr1 21 30
chr1 11 20 chr1 51 55
chr1 11 30 chr1 51 55
chr1 11 30 chr2 51 60",
col.names = c(
"seqnames1", "start1", "end1",
"seqnames2", "start2", "end2")
) |>
as_ginteractions() |>
mutate(type = c('cis', 'cis', 'cis', 'trans'), score = runif(4))
####################################################################
# 1. Replace anchors of a GInteractions object
####################################################################
gi |> replace_anchors(2, value = anchors1(gi))
#> GInteractions object with 4 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 11-20 * --- chr1 11-20 * | cis
#> [2] chr1 11-20 * --- chr1 11-20 * | cis
#> [3] chr1 11-30 * --- chr1 11-30 * | cis
#> [4] chr1 11-30 * --- chr1 11-30 * | trans
#> score
#> <numeric>
#> [1] 0.3900314
#> [2] 0.0200652
#> [3] 0.3769709
#> [4] 0.5599128
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> replace_anchors(1, value = anchors2(gi))
#> GInteractions object with 4 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 21-30 * --- chr1 21-30 * | cis
#> [2] chr1 51-55 * --- chr1 51-55 * | cis
#> [3] chr1 51-55 * --- chr1 51-55 * | cis
#> [4] chr2 51-60 * --- chr2 51-60 * | trans
#> score
#> <numeric>
#> [1] 0.3900314
#> [2] 0.0200652
#> [3] 0.3769709
#> [4] 0.5599128
#> -------
#> regions: 3 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> replace_anchors(1, value = GenomicRanges::GRanges(c(
"chr1:1-2", "chr1:2-3", "chr1:3-4", "chr1:4-5"
)))
#> GInteractions object with 4 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 1-2 * --- chr1 21-30 * | cis
#> [2] chr1 2-3 * --- chr1 51-55 * | cis
#> [3] chr1 3-4 * --- chr1 51-55 * | cis
#> [4] chr1 4-5 * --- chr2 51-60 * | trans
#> score
#> <numeric>
#> [1] 0.3900314
#> [2] 0.0200652
#> [3] 0.3769709
#> [4] 0.5599128
#> -------
#> regions: 7 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. Replace anchors of a pinned GInteractions object
####################################################################
gi |> pin_by(1) |> replace_anchors(value = anchors1(gi))
#> PinnedGInteractions object with 4 interactions and 2 metadata columns:
#> Pinned on: anchors1
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 11-20 * --- chr1 21-30 * | cis
#> [2] chr1 11-20 * --- chr1 51-55 * | cis
#> [3] chr1 11-30 * --- chr1 51-55 * | cis
#> [4] chr1 11-30 * --- chr2 51-60 * | trans
#> score
#> <numeric>
#> [1] 0.3900314
#> [2] 0.0200652
#> [3] 0.3769709
#> [4] 0.5599128
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> replace_anchors(1, value = anchors2(gi))
#> GInteractions object with 4 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 21-30 * --- chr1 21-30 * | cis
#> [2] chr1 51-55 * --- chr1 51-55 * | cis
#> [3] chr1 51-55 * --- chr1 51-55 * | cis
#> [4] chr2 51-60 * --- chr2 51-60 * | trans
#> score
#> <numeric>
#> [1] 0.3900314
#> [2] 0.0200652
#> [3] 0.3769709
#> [4] 0.5599128
#> -------
#> regions: 3 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |>
pin_by(1) |>
replace_anchors(value = GenomicRanges::GRanges(c(
"chr1:1-2", "chr1:2-3", "chr1:3-4", "chr1:4-5"
))) |>
pin_by(2) |>
replace_anchors(value = GenomicRanges::GRanges(c(
"chr2:1-2", "chr2:2-3", "chr2:3-4", "chr2:4-5"
)))
#> PinnedGInteractions object with 4 interactions and 2 metadata columns:
#> Pinned on: anchors2
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 1-2 * --- chr2 1-2 * | cis
#> [2] chr1 2-3 * --- chr2 2-3 * | cis
#> [3] chr1 3-4 * --- chr2 3-4 * | cis
#> [4] chr1 4-5 * --- chr2 4-5 * | trans
#> score
#> <numeric>
#> [1] 0.3900314
#> [2] 0.0200652
#> [3] 0.3769709
#> [4] 0.5599128
#> -------
#> regions: 8 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths