Flag twin inversions

Flag ranges that start a quadruplet that would be colinear if the two central pairs were aligned to the opposite strand. This implies breakpoint reuse.

Usage

flagTwinInversions(gb, details = FALSE)

Arguments

gb

A GBreaks() object.

details

Returns more metadata columns if TRUE.

Value

Returns the GBreaks object with an extra twi metadata column.

Details

Here is a trivial example of a twin inversion.

┌──────────────┬──────────────┬──────────────┐──────────────┐
│ chrA:101-200 │ chrA:201-300 │ chrA:301-400 │ chrA:401-500 │ (Target genome)
└──────────────┴──────────────┴──────────────┘──────────────┘
       +               -             -              +   (Alignment direction)
┌──────────────┬──────────────┬──────────────┐──────────────┐
│ chrB:101-200 │ chrB:201-300 │ chrB:301-400 │ chrB:401-500 │  (Query genome)
└──────────────┴──────────────┴──────────────┘──────────────┘

See also

Other Flagging functions: flagAll(), flagColinearAlignments(), flagDoubleInversions(), flagInversions(), flagLongShort(), flagPairs(), flagTranslocations()

Other Inversion functions: filterDoubleInversions(), filterInversions(), flagDoubleInversions(), flagInversions(), flagPairs(), flipInversions(), leftInversionGaps(), removeDoubleInversions(), removeInversions(), showInversions()

Other Structural variants: StructuralVariants, flagDoubleInversions(), flagInversions(), flagPairs(), flagTranslocations(), plotApairOfChrs()

Examples

flagTwinInversions(exampleTwinInversions)
#> GBreaks object with 4 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query       twi
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <logical>
#>   [1]     chrA   100-190      + | chrB:100-190      TRUE
#>   [2]     chrA   200-290      - | chrB:200-290     FALSE
#>   [3]     chrA   300-390      - | chrB:300-390     FALSE
#>   [4]     chrA   400-490      + | chrB:400-490     FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
plotApairOfChrs(exampleTwinInversions)


flagTwinInversions(exampleTwinInversions |> reverse() |> sort(ignore.strand = TRUE))
#> GBreaks object with 4 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query       twi
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <logical>
#>   [1]     chrA   111-201      - | chrB:400-490      TRUE
#>   [2]     chrA   211-301      + | chrB:300-390     FALSE
#>   [3]     chrA   311-401      + | chrB:200-290     FALSE
#>   [4]     chrA   411-501      - | chrB:100-190     FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
plotApairOfChrs(exampleTwinInversions |> reverse())