Get each set from a MergedGInteractions object

Returns the subset of MergedGInteractions that belong to each input source object (see these with `sources(x)`). If the source pairs all come from the same object, their corresponding merged pair is returned. However, if at least one source pair comes from a different object, then that merged pair is not returned.

Usage

sets(x, include, exclude)

# S4 method for MergedGInteractions,missing,missing
sets(x)

# S4 method for MergedGInteractions,character_OR_missing,missing
sets(x, include)

# S4 method for MergedGInteractions,missing,character_OR_missing
sets(x, exclude)

# S4 method for MergedGInteractions,character_OR_missing,character_OR_missing
sets(x, include, exclude)

Arguments

x

MergedGInteractions object.

include

(Optional) A character vector of sources in which a pair must be present. For a list of available sources use `sources(x)`.

exclude

(Optional) A character vector of sources in which a pair must be absent. For a list of available sources use `sources(x)`.

Value

A list of subsetted `MergedGInteractions` objects or a `MergedGInteractions` object (if `include` and/or `exclude` are used).

Details

Optional `include` and `exclude` parameters modulate the behavior of `sets` to return different subsets of originating pairs. For example, `include` requires that the returned pairs be present in specific sources, while `exclude` requires that returned pairs be absent from specific sources. Sources not listed in either `include` or `exclude` are ignored (they may or may not) be present in the returned `MergedGInteractions` object. `include` and `exclude` can be used indepedently or in combination to return every possible set. If any of the same sources are used in both `include` and `exclude` the function will return a 0-length MergedGInteractions object.

Examples

## Load required packages
library(GenomicRanges)
library(InteractionSet)

## Define example anchor regions
gr1 <-
    GRanges(seqnames = "chr1",
            ranges = IRanges(start = c(30,40,40,70,80),
                             end = c(40,50,50,80,90)))
gr2 <-
    GRanges(seqnames = "chr1",
            ranges = IRanges(start = c(30,30,50,10,30),
                             end = c(40,40,60,20,40)))

## Form GInteractions and split into two files
giList <- split(x = GInteractions(gr1, gr2),
                f = c(rep(1,3), rep(2,2)))

## Merge pairs
x <- mergePairs(x = giList, radius = 20)

sets(x)
#> $`1`
#> MergedGInteractions object with 1 interaction and 0 metadata columns:
#>       seqnames1   ranges1     seqnames2   ranges2
#>           <Rle> <IRanges>         <Rle> <IRanges>
#>   [1]      chr1     40-50 ---      chr1     30-40
#>   -------
#>   regions: 5 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> $`2`
#> MergedGInteractions object with 2 interactions and 0 metadata columns:
#>       seqnames1   ranges1     seqnames2   ranges2
#>           <Rle> <IRanges>         <Rle> <IRanges>
#>   [1]      chr1     70-80 ---      chr1     10-20
#>   [2]      chr1     80-90 ---      chr1     30-40
#>   -------
#>   regions: 5 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> 
#> $`1_2`
#> MergedGInteractions object with 0 interactions and 0 metadata columns:
#>    seqnames1   ranges1     seqnames2   ranges2
#>        <Rle> <IRanges>         <Rle> <IRanges>
#>   -------
#>   regions: 5 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>