calcPairs.RdcalcPairs will calculate pairs of interactions within a rolling windowSize. By default, pairs of interactions are returned as StrictGInteractions where anchor1 <= anchor2 for all interactions (mode = 'strict'). For more information see (?InteractionSet::`GInteractions-class`). Self interactions (e.g. 1, 1 or 2, 2) and order (e.g. 1, 2 is the same as 2, 1) are ignored.
calcPairs(gr, windowSize, mode = "strict")GRanges object
integer defining the window
If mode="strict", a StrictGInterctions object is returned with anchor indices swapped such that anchor1 <= anchor2 for all interactions. If mode="reverse", a ReverseStrictGInterctions object is returned with anchor indices swapped such that anchor1 >= anchor2.
Returns a StrictGInterations object
## Load TxDb
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#> Loading required package: GenomicFeatures
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
## Generate 50Kb bins across hg19
library(GenomicRanges)
bins <- tileGenome(seqinfo(txdb), tilewidth = 50e3, cut.last.tile.in.chrom = TRUE)
## Calculate all 50Kb bin pairs within 1Mb
calcPairs(gr = bins, windowSize = 1e6)
#>
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#>
#> StrictGInteractions object with 1184080 interactions and 0 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2
#> <Rle> <IRanges> <Rle> <IRanges>
#> [1] chr1 1-50000 --- chr1 50001-100000
#> [2] chr1 1-50000 --- chr1 100001-150000
#> [3] chr1 1-50000 --- chr1 150001-200000
#> [4] chr1 1-50000 --- chr1 200001-250000
#> [5] chr1 1-50000 --- chr1 250001-300000
#> ... ... ... ... ... ...
#> [1184076] chrUn_gl000227 1-50000 --- chrUn_gl000227 100001-128374
#> [1184077] chrUn_gl000227 50001-100000 --- chrUn_gl000227 100001-128374
#> [1184078] chrUn_gl000228 1-50000 --- chrUn_gl000228 50001-100000
#> [1184079] chrUn_gl000228 1-50000 --- chrUn_gl000228 100001-129120
#> [1184080] chrUn_gl000228 50001-100000 --- chrUn_gl000228 100001-129120
#> -------
#> regions: 62783 ranges and 0 metadata columns
#> seqinfo: 93 sequences (1 circular) from hg19 genome