Flag inversions

Flag ranges that start a triplet that would be colinear if the central pair were aligned to the opposite strand.

Usage

flagInversions(gb, tol = Inf)

Arguments

gb

A GBreaks() object.

tol

Tolerance window for the distance between two ranges.

Value

Returns the GBreaks object with an extra inv metadata column.

Details

Here is a trivial example of an inversion.

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

See also

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

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

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

Examples

flagInversions(exampleInversion)
#> GBreaks object with 3 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query   inv
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <Rle>
#>   [1]     chrA   100-190      + | chrB:100-190  TRUE
#>   [2]     chrA   210-291      - | chrB:210-291 FALSE
#>   [3]     chrA   301-400      + | chrB:301-400 FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
flagInversions(exampleInversion, tol = 19)
#> GBreaks object with 3 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query   inv
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <Rle>
#>   [1]     chrA   100-190      + | chrB:100-190 FALSE
#>   [2]     chrA   210-291      - | chrB:210-291 FALSE
#>   [3]     chrA   301-400      + | chrB:301-400 FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
plotApairOfChrs(exampleInversion)


flagInversions(exampleInversion |> reverse() |> sort(ignore.strand = TRUE))
#> GBreaks object with 3 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query   inv
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <Rle>
#>   [1]     chrA   201-300      - | chrB:301-400  TRUE
#>   [2]     chrA   310-391      + | chrB:210-291 FALSE
#>   [3]     chrA   411-501      - | chrB:100-190 FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
plotApairOfChrs(exampleInversion |> reverse())