Extract central blocks in inversions

Extract central blocks in inversions

Usage

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

Arguments

gb

A GBreaks.

rename

Replace range names by their numeric order before subsetting.

detect

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

Value

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

See also

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

Examples

filterInversions(exampleInversion)
#> GBreaks object with 1 range and 2 metadata columns:
#>     seqnames    ranges strand |        query   inv
#>        <Rle> <IRanges>  <Rle> |    <GRanges> <Rle>
#>   2     chrA   210-291      - | chrB:210-291 FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome