Annotate both anchors of a GInteractions
Source:R/AllGenerics.R, R/annotate.R
ginteractions-annotate.RdFor each interaction in a GInteractions object, annotate returns
the pairs of annotations from the GRanges object it overlaps with.
Usage
annotate(x, y, by)
annotate_directed(x, y, by)
# S4 method for class 'GInteractions,GRanges,character'
annotate(x, y, by)
# S4 method for class 'GInteractions,GRanges,character'
annotate_directed(x, y, by)Examples
####################################################################
# 1. Basic example
####################################################################
gi <- read.table(text = "
chr1 11 20 - chr1 21 30 +
chr1 21 30 + chr2 51 60 +",
col.names = c(
"seqnames1", "start1", "end1", "strand1",
"seqnames2", "start2", "end2", "strand2"
)
) |> as_ginteractions()
gr <- GenomicRanges::GRanges(c("chr1:20-30:+", "chr2:55-65:+")) |>
plyranges::mutate(id = 1:2)
annotate(gi, gr, by = 'id')
#> GInteractions object with 2 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.1
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | 1
#> [2] chr1 21-30 + --- chr2 51-60 + | 1
#> id.2
#> <integer>
#> [1] 1
#> [2] 2
#> -------
#> regions: 3 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
annotate_directed(gi, gr, by = 'id')
#> GInteractions object with 2 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | id.1
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 11-20 - --- chr1 21-30 + | <NA>
#> [2] chr1 21-30 + --- chr2 51-60 + | 1
#> id.2
#> <integer>
#> [1] 1
#> [2] 2
#> -------
#> regions: 3 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. Match loops with tiled genomic bins
####################################################################
data(GM12878_HiCCUPS)
loops <- GM12878_HiCCUPS |>
pin_by('first') |>
anchor_center() |>
mutate(width1 = 500) |>
pin_by('second') |>
anchor_center() |>
mutate(width2 = 500)
genomic_bins <- GenomeInfoDb::getChromInfoFromUCSC(
'hg19', assembled.molecules.only = TRUE, as.Seqinfo = TRUE
) |>
GenomicRanges::tileGenome(tilewidth = 10000) |>
unlist() |>
plyranges::mutate(binID = seq_len(plyranges::n()))
annotate(loops, genomic_bins, by = 'binID') |>
select(starts_with('binID'))
#> GInteractions object with 10898 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2
#> <Rle> <IRanges> <Rle> <Rle>
#> [1] chr10 100227250-100227749 * --- chr10
#> [2] chr10 100227250-100227749 * --- chr10
#> [3] chr10 101192250-101192749 * --- chr10
#> [4] chr10 101194750-101195249 * --- chr10
#> [5] chr10 101602250-101602749 * --- chr10
#> ... ... ... ... ... ...
#> [10894] chrX 9847250-9847749 * --- chrX
#> [10895] chrX 9847250-9847749 * --- chrX
#> [10896] chrX 9962250-9962749 * --- chrX
#> [10897] chrX 99764750-99765249 * --- chrX
#> [10898] chrX 99942250-99942749 * --- chrX
#> ranges2 strand2 | binID.1 binID.2
#> <IRanges> <Rle> | <integer> <integer>
#> [1] 100422250-100422749 * | 178070 178090
#> [2] 101007250-101007749 * | 178070 178148
#> [3] 101372250-101372749 * | 178167 178185
#> [4] 101474750-101475249 * | 178167 178195
#> [5] 101807250-101807749 * | 178208 178228
#> ... ... ... . ... ...
#> [10894] 10087250-10087749 * | 289111 289135
#> [10895] 9962250-9962749 * | 289111 289123
#> [10896] 10087250-10087749 * | 289123 289135
#> [10897] 100024750-100025249 * | 298103 298129
#> [10898] 100022250-100022749 * | 298121 298129
#> -------
#> regions: 16123 ranges and 0 metadata columns
#> seqinfo: 23 sequences from an unspecified genome; no seqlengths
####################################################################
# 3. Annotate interactions by a set of regulatory elements
####################################################################
data(ce10_ARCC)
data(ce10_REs)
annotate(ce10_ARCC, ce10_REs, by = 'annot') |>
count(annot.1, annot.2) |>
as.data.frame() |>
dplyr::arrange(desc(n))
#> annot.1 annot.2 n
#> 1 coding_promoter coding_promoter 5563
#> 2 coding_promoter putative_enhancer 2546
#> 3 putative_enhancer coding_promoter 2540
#> 4 putative_enhancer putative_enhancer 1814
#> 5 coding_promoter unassigned_promoter 809
#> 6 unassigned_promoter coding_promoter 753
#> 7 putative_enhancer unassigned_promoter 566
#> 8 unassigned_promoter putative_enhancer 533
#> 9 non-coding_RNA coding_promoter 247
#> 10 coding_promoter non-coding_RNA 242
#> 11 unassigned_promoter unassigned_promoter 209
#> 12 coding_promoter other_element 188
#> 13 other_element coding_promoter 173
#> 14 other_element putative_enhancer 115
#> 15 non-coding_RNA putative_enhancer 110
#> 16 putative_enhancer other_element 100
#> 17 putative_enhancer non-coding_RNA 93
#> 18 <NA> coding_promoter 54
#> 19 pseudogene_promoter coding_promoter 45
#> 20 putative_enhancer <NA> 44
#> 21 non-coding_RNA non-coding_RNA 43
#> 22 non-coding_RNA unassigned_promoter 41
#> 23 coding_promoter pseudogene_promoter 40
#> 24 coding_promoter <NA> 39
#> 25 other_element unassigned_promoter 36
#> 26 other_element other_element 32
#> 27 <NA> putative_enhancer 32
#> 28 unassigned_promoter non-coding_RNA 25
#> 29 unassigned_promoter other_element 25
#> 30 other_element non-coding_RNA 19
#> 31 <NA> <NA> 19
#> 32 non-coding_RNA other_element 16
#> 33 putative_enhancer pseudogene_promoter 16
#> 34 unassigned_promoter <NA> 13
#> 35 pseudogene_promoter putative_enhancer 11
#> 36 <NA> unassigned_promoter 10
#> 37 pseudogene_promoter unassigned_promoter 9
#> 38 other_element pseudogene_promoter 6
#> 39 pseudogene_promoter pseudogene_promoter 5
#> 40 other_element <NA> 3
#> 41 unassigned_promoter pseudogene_promoter 3
#> 42 non-coding_RNA <NA> 2
#> 43 pseudogene_promoter non-coding_RNA 2
#> 44 pseudogene_promoter other_element 1
#> 45 <NA> non-coding_RNA 1
#> 46 <NA> other_element 1