Flexibly bin paired ranges

Paired range objects (like `GInteractions` or BEDPE-formatted `data.frame`-like objects) can be binned separately for each set of ranges.

Usage

assignToBins(x, binSize, pos1 = "center", pos2 = "center", ...)

# S4 method for DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing
assignToBins(x, binSize, pos1, pos2)

# S4 method for GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing
assignToBins(x, binSize, pos1, pos2)

Arguments

x

`GInteractions` or `data.frame`-like object with paired interactions.

binSize

Integer (numeric) vector describing the new size of each pair of ranges. Accepts up to 2 values for adjusting each pair.

pos1, pos2

Position within anchors to resize the bin. Can be a character or integer vector of length 1 or `length(x)` designating the position for each element in `x`. Character options are "start", "end" and "center". Integers are referenced from the start position for '+' and '*' strands and from the end position for the '-' strand.

...

Additional arguments.

Value

GInteractions-like object binned to `binSize` by `pos1` and `pos2`.

Examples

## Construct interactions as data.frame
df1 <-
    data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
               chr2 = "chr1", y1 = 30000, y2 = 40000)

## Assign each range to 20-kb bins from the start positions
assignToBins(x = df1,
         binSize = 20000,
         pos1 = 'start',
         pos2 = 'start')
#> GInteractions object with 1 interaction and 0 metadata columns:
#>       seqnames1   ranges1     seqnames2     ranges2
#>           <Rle> <IRanges>         <Rle>   <IRanges>
#>   [1]      chr1   0-20000 ---      chr1 20000-40000
#>   -------
#>   regions: 2 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

## Construct GInteractions
library(InteractionSet)
gi1 <-
    data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
               chr2 = "chr1", y1 = 30000, y2 = 40000) |>
    as_ginteractions()

## Assign each range to 20-kb bins from the start positions
assignToBins(x = gi1,
         binSize = 20000,
         pos1 = 'start',
         pos2 = 'start')
#> GInteractions object with 1 interaction and 0 metadata columns:
#>       seqnames1   ranges1     seqnames2     ranges2
#>           <Rle> <IRanges>         <Rle>   <IRanges>
#>   [1]      chr1   0-20000 ---      chr1 20000-40000
#>   -------
#>   regions: 2 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths