Remove translocations

Remove translocations

Usage

removeTranslocations(gb, detect = TRUE)

Arguments

gb

A GBreaks object.

detect

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

Value

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

See also

Other Translocation functions: filterTranslocations(), flagTranslocations(), showTranslocations()

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

Examples

removeTranslocations(exampleTranslocation)
#> 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