Compute all flags

Flag ranges that are at the beginning of a colinear duplet, or an inversion or a translocation triplet.

Usage

flagAll(gb)

Arguments

gb

A GBreaks object.

Value

Returns the GBreaks object with an extra flag metadata column.

See also

Other Flagging functions: flagColinearAlignments(), flagDoubleInversions(), flagInversions(), flagLongShort(), flagPairs(), flagTranslocations()

Examples

flagAll(exampleInversion)
#> GBreaks object with 3 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query        flag
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <character>
#>   [1]     chrA   100-190      + | chrB:100-190         Inv
#>   [2]     chrA   210-291      - | chrB:210-291        <NA>
#>   [3]     chrA   301-400      + | chrB:301-400        <NA>
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome