Drop loops from LoopRanges objects using anchor and loop sizes

Subset loops based on loop and anchor size filters. Can be used to filter the loops in the LoopRanges object before or after calling ConsensusLoops

DropLoops(loop_ranges, type = NULL, size = NULL)

Arguments

loop_ranges	A LoopRanges class object
type	A string indicating the type of filtering when determining which loops to drop: "anchor_size" - Drops loops based on given anchor sizes "loop_size" - Drops loops based on end-to-end loop size
size	A numerical vector indicating size range to keep (e.g. c(start, end))

Value

A subsetted LoopRanges class object

Examples

# Load loops into LoopRanges object 
ovary_loops <- system.file("extdata/loops", "ovary_hg19.bedpe",
package = "LoopRig", mustWork = TRUE)
loops_ovary <- LoopsToRanges(ovary_loops, custom_cols = 0)

# Subset loops based on total length between 100 to 100000 bp 
DropLoops(loops_ovary, type = "loop_size", size = c(100, 100000))
#> [[1]]
#> GRangesList object of length 2:
#> $Anchor 1 
#> GRanges object with 1478 ranges and 0 metadata columns:
#>          seqnames              ranges strand
#>             <Rle>           <IRanges>  <Rle>
#>      [1]     chr5   29850107-29860107      *
#>      [2]     chr5 158207008-158217008      *
#>      [3]     chr5 158367008-158377008      *
#>      [4]     chr5 121665695-121675695      *
#>      [5]     chr5   77835823-77845823      *
#>      ...      ...                 ...    ...
#>   [1474]     chr4 180481153-180491153      *
#>   [1475]     chr4 119811155-119821155      *
#>   [1476]     chr4 188531154-188541154      *
#>   [1477]     chr4 171841151-171851151      *
#>   [1478]     chr4   20001623-20011623      *
#> 
#> ...
#> <1 more element>
#> -------
#> seqinfo: 23 sequences from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "LoopRanges"

# Subset loops based on anchor size between 1000 to 25000 bp 
DropLoops(loops_ovary, type = "anchor_size", size = c(1000, 25000))
#> [[1]]
#> GRangesList object of length 2:
#> $Anchor 1 
#> GRanges object with 5647 ranges and 0 metadata columns:
#>          seqnames              ranges strand
#>             <Rle>           <IRanges>  <Rle>
#>      [1]     chr5   14140109-14150109      *
#>      [2]     chr5   29850107-29860107      *
#>      [3]     chr5 158137008-158147008      *
#>      [4]     chr5 158197008-158207008      *
#>      [5]     chr5 158167008-158177008      *
#>      ...      ...                 ...    ...
#>   [5643]     chr4   78621154-78631154      *
#>   [5644]     chr4   33601622-33611622      *
#>   [5645]     chr4   41452017-41462017      *
#>   [5646]     chr4   99321151-99331151      *
#>   [5647]     chr4 169501151-169511151      *
#> 
#> ...
#> <1 more element>
#> -------
#> seqinfo: 23 sequences from an unspecified genome; no seqlengths
#> 
#> attr(,"class")
#> [1] "LoopRanges"