subsetByOverlaps method for GBreaks objects

This is a subsetByOverlaps method for GBreaks objects, that will run GenomicRanges::subsetByOverlaps on its target and query ranges and will return a new GBreaks object.

Usage

subsetByOverlaps_GBreaks(
  x,
  ranges,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  invert = FALSE,
  ...
)

# S4 method for GBreaks,GBreaks
subsetByOverlaps(
  x,
  ranges,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  invert = FALSE,
  ...
)

Arguments

x

A GBreaks object.

ranges

Another GBreaks object.

maxgap

tbd

minoverlap

tbd

type

tbd

invert

tbd

...

etc

Value

tbd

Note

range unconditionally ignores strand in GBreaks objects.

See also

Other Bioconductor API functions: GBreaks-class, as(), getSeq(), pairwiseAlignment(), range_GBreaks(), reverse()

Examples

subsetByOverlaps(exampleColinear3, exampleColinear3)
#> GBreaks object with 3 ranges and 1 metadata column:
#>       seqnames    ranges strand |        query
#>          <Rle> <IRanges>  <Rle> |    <GRanges>
#>   [1]     chrA   100-200      + | chrB:100-200
#>   [2]     chrA   201-300      + | chrB:201-300
#>   [3]     chrA   301-400      + | chrB:301-400
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome