Remove inversions

Remove inversions

Usage

removeInversions(gb, detect = TRUE)

Arguments

gb

A GBreaks object.

detect

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

Value

Returns the GBreaks object after removing the ranges that are inverted and coalescing the resulting collinear ranges.

See also

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

Other modifier functions: bridgeRegions(), coalesce_contigs(), flipInversions(), forceSeqLengths(), guessSeqLengths(), keepLongestPair(), matchPairs(), mergeSeqLevels(), removeDoubleInversions(), removeTranslocations(), reverse(), splitSeqLevel(), swap()

Examples

removeInversions(exampleInversion)
#> GBreaks object with 1 range and 2 metadata columns:
#>       seqnames    ranges strand |        query     score
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <integer>
#>   [1]     chrA   100-400      + | chrB:100-400       301
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome