Manage GInteractions anchors with plyranges
Usage
# S3 method for class 'AnchoredPinnedGInteractions'
anchor(x)
# S3 method for class 'AnchoredPinnedGInteractions'
unanchor(x)
# S3 method for class 'PinnedGInteractions'
anchor_start(x)
# S3 method for class 'PinnedGInteractions'
anchor_end(x)
# S3 method for class 'PinnedGInteractions'
anchor_center(x)
# S3 method for class 'PinnedGInteractions'
anchor_3p(x)
# S3 method for class 'PinnedGInteractions'
anchor_5p(x)
# S3 method for class 'AnchoredPinnedGInteractions'
anchor_start(x)
# S3 method for class 'AnchoredPinnedGInteractions'
anchor_end(x)
# S3 method for class 'AnchoredPinnedGInteractions'
anchor_center(x)
# S3 method for class 'AnchoredPinnedGInteractions'
anchor_3p(x)
# S3 method for class 'AnchoredPinnedGInteractions'
anchor_5p(x)Value
anchor_*functions return an AnchoredPinnedGInteractions object.anchorreturns a character string indicating where the pinned anchors are anchored at.unanchorremoves the anchoring for a AnchoredPinnedGInteractions object.
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", "strand1", "strand2")
) |>
as_ginteractions() |>
mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans'))
gi
#> GInteractions object with 4 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 11-20 + --- chr1 21-30 + | 0.0280610
#> [2] chr1 11-20 + --- chr1 51-55 + | 0.4659872
#> [3] chr1 11-30 - --- chr1 51-55 - | 0.3900314
#> [4] chr1 11-30 - --- chr2 51-60 - | 0.0200652
#> type
#> <character>
#> [1] cis
#> [2] cis
#> [3] cis
#> [4] trans
#> -------
#> regions: 6 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 1. Anchoring pinned genomic interactions with plyranges
####################################################################
gi |> pin_by("second") |> anchor_end()
#> AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns:
#> Pinned on: anchors2 | Anchored by: end
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 11-20 + --- chr1 21-30 + | 0.0280610
#> [2] chr1 11-20 + --- chr1 51-55 + | 0.4659872
#> [3] chr1 11-30 - --- chr1 51-55 - | 0.3900314
#> [4] chr1 11-30 - --- chr2 51-60 - | 0.0200652
#> type
#> <character>
#> [1] cis
#> [2] cis
#> [3] cis
#> [4] trans
#> -------
#> regions: 6 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> pin_by("first") |> anchor_start()
#> AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns:
#> Pinned on: anchors1 | Anchored by: start
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 11-20 + --- chr1 21-30 + | 0.0280610
#> [2] chr1 11-20 + --- chr1 51-55 + | 0.4659872
#> [3] chr1 11-30 - --- chr1 51-55 - | 0.3900314
#> [4] chr1 11-30 - --- chr2 51-60 - | 0.0200652
#> type
#> <character>
#> [1] cis
#> [2] cis
#> [3] cis
#> [4] trans
#> -------
#> regions: 6 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |>
pin_by("first") |> anchor_center() |> stretch(4) |>
pin_by("second") |> anchor_3p() |> stretch(-2)
#> PinnedGInteractions object with 4 interactions and 2 metadata columns:
#> Pinned on: anchors2
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 9-22 + --- chr1 23-30 + | 0.0280610
#> [2] chr1 9-22 + --- chr1 53-55 + | 0.4659872
#> [3] chr1 9-32 - --- chr1 51-53 - | 0.3900314
#> [4] chr1 9-32 - --- chr2 51-58 - | 0.0200652
#> type
#> <character>
#> [1] cis
#> [2] cis
#> [3] cis
#> [4] trans
#> -------
#> regions: 6 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths