connectLoopAnchors

connectLoopAnchors

Usage

connectLoopAnchors(loops, overlapDist)

Arguments

loops

GInteractions object of loops

overlapDist

an integer representing the farthest distance in base pairs to make a connection

Value

GInteractions object

Examples

mergedLoops <- mergeAnchors(GM12878_10KbLoops, 1)

connectLoopAnchors(mergedLoops, 1e6)
#> GInteractions object with 1523 interactions and 1 metadata column:
#>          seqnames1           ranges1     seqnames2           ranges2 |
#>              <Rle>         <IRanges>         <Rle>         <IRanges> |
#>      [1]        22 17400000-17410000 ---        22 17530000-17540000 |
#>      [2]        22 17400000-17410000 ---        22 17650000-17660000 |
#>      [3]        22 17400000-17410000 ---        22 17980000-17990000 |
#>      [4]        22 17400000-17410000 ---        22 18310000-18320000 |
#>      [5]        22 17530000-17540000 ---        22 17650000-17660000 |
#>      ...       ...               ... ...       ...               ... .
#>   [1519]        22 50930000-50940000 ---        22 51070000-51080000 |
#>   [1520]        22 50930000-50940000 ---        22 51130000-51140000 |
#>   [1521]        22 51050000-51060000 ---        22 51070000-51080000 |
#>   [1522]        22 51050000-51060000 ---        22 51130000-51140000 |
#>   [1523]        22 51070000-51080000 ---        22 51130000-51140000 |
#>               source
#>          <character>
#>      [1]    original
#>      [2]       added
#>      [3]    original
#>      [4]       added
#>      [5]       added
#>      ...         ...
#>   [1519]       added
#>   [1520]       added
#>   [1521]       added
#>   [1522]       added
#>   [1523]    original
#>   -------
#>   regions: 224 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths