Extract central blocks in double inversions

Extract central blocks in double inversions

Usage

filterDoubleInversions(gb, rename = TRUE, detect = TRUE)

Arguments

gb

A GBreaks object.

rename

Replace range names by their numeric order before subsetting.

detect

Run again flagDoubleInversions() if TRUE, else reuse the Dbl flag or fail if it is absent.

Value

Returns the GBreaks object in which all ranges that are not the central part of a double inversion quintuplet have been discarded. If the object was missing the Dbl metadata column, return the object after discarding all of its ranges.

See also

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

Examples

filterDoubleInversions(exampleDoubleInversion1)
#> GBreaks object with 3 ranges and 2 metadata columns:
#>     seqnames    ranges strand |        query       Dbl
#>        <Rle> <IRanges>  <Rle> |    <GRanges> <logical>
#>   3     chrA   300-390      - | chrB:200-290     FALSE
#>   4     chrA   400-490      - | chrB:300-390     FALSE
#>   5     chrA   500-590      + | chrB:500-590     FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome