Build a GInteractions object with all pairs of input GRanges within a given distance.

Distance is calculated from the center of input regions.

getCisPairs(inGR, maxDist = 1e+06)

Arguments

inGR	GRanges object of genomic regions. The ranges should be sorted according to chr, strand, and start position. Use sort to sort it.
maxDist	maximal distance in base-pairs between pairs of ranges as single numeric value.

Value

A GInteractions object with all pairs within the given distance.

Examples

# build example GRanges as input
inGR <- GRanges(
rep("chr1", 5),
IRanges(
  c(10, 20, 30, 100, 1000),
  c(15, 25, 35, 105, 1005)
)
)

# get all pairs within 50 bp
gi <- getCisPairs(inGR, maxDist = 50)

# getCisPiars returns a StrictGInteractions object
class(gi)
#> [1] "StrictGInteractions"
#> attr(,"package")
#> [1] "InteractionSet"

# The input regions are accessibly via regions()
regions(gi)
#> GRanges object with 5 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1     10-15      *
#>   [2]     chr1     20-25      *
#>   [3]     chr1     30-35      *
#>   [4]     chr1   100-105      *
#>   [5]     chr1 1000-1005      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths