Match pairs of sequences

For each sequence of the target genome, assign a sequence of the query genome, and discard all the ranges that are not from matched pairs.

Usage

matchPairs(gb, drop = FALSE)

Arguments

gb

A GBreaks object.

drop

Drop unused sequence levels.

Value

A GBreaks object.

Note

This is not a reciprocal best match function, because it assumes that the genomes are close enough and that there were no major karyotype changes, so that the pairing is a trivial operation.

See also

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

Author

Charles Plessy

Examples

matchPairs(exampleTranslocation)
#> GBreaks object with 2 ranges and 1 metadata column:
#>        seqnames    ranges strand |        query
#>           <Rle> <IRanges>  <Rle> |    <GRanges>
#>   chrA     chrA   100-200      + | chrB:100-200
#>   chrA     chrA   301-400      + | chrB:301-400
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome