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Get breakpoints

Source: R/get_bps.R
get_bps.Rd

Given a GBreaks or GenomicRanges::GRanges object, the function produces a GRanges object detailing the breakpoints only.

Usage

get_bps(
  gr,
  direction = c("both", "left", "right", "mid"),
  stranded = FALSE,
  sorted = TRUE
)

Arguments

gr

GRanges object containing pairwise alignment

direction

Return the breakpoints on both, left or right side(s) of the range, or at the midpoint between ranges.

stranded

If TRUE, will assign a + strand to the left-side breakpoints and a - strand to the right-side ones.

sorted

Sorts the object before returning it.

Value

GRanges object of the breakpoints

See also

Other Reducing functions: cleanGaps(), wholeGenomeClassification()

Examples

get_bps(exampleInversion)
#> GRanges object with 6 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chrA       100      *
#>   [2]     chrA       190      *
#>   [3]     chrA       210      *
#>   [4]     chrA       291      *
#>   [5]     chrA       301      *
#>   [6]     chrA       400      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
get_bps(exampleInversion, direction = "left")
#> GRanges object with 3 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chrA       100      *
#>   [2]     chrA       210      *
#>   [3]     chrA       301      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
get_bps(exampleInversion, stranded = TRUE)
#> GRanges object with 6 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chrA       100      +
#>   [2]     chrA       190      -
#>   [3]     chrA       210      +
#>   [4]     chrA       291      -
#>   [5]     chrA       301      +
#>   [6]     chrA       400      -
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
get_bps(exampleInversion, direction = "right", stranded = TRUE)
#> GRanges object with 3 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chrA       190      -
#>   [2]     chrA       291      -
#>   [3]     chrA       400      -
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
get_bps(exampleInversion, direction = "mid")
#> GRanges object with 2 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chrA       200      *
#>   [2]     chrA       296      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome