Hi everyone, I needed some help using GenomicRanges from R.

I have Two gr objects such as :

> genes_bacteria
GRanges object with 6 ranges and 0 metadata columns:
        seqnames    ranges strand
           <Rle> <IRanges>  <Rle>
  [1] scaffold_1      1-50      -
  [2] scaffold_1    60-100      -
  [3] scaffold_1   200-350      -
  [4] scaffold_2 1500-1700      +
  [5] scaffold_2 1900-2300      -
  [6] scaffold_5   250-255      +
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

and

> genes_busco
GRanges object with 6 ranges and 0 metadata columns:
        seqnames    ranges strand
           <Rle> <IRanges>  <Rle>
  [1] scaffold_1      1-50      +
  [2] scaffold_1    70-120      +
  [3] scaffold_2 1550-1650      +
  [4] scaffold_3 3000-3815      +
  [5] scaffold_4     6-251      +
  [6] scaffold_5     6-251      -
  -------
  seqinfo: 5 sequences from an unspecified genome; no seqlengths

I found the overlapping sequences between them by using the following code:

hits <- findOverlaps(genes_bacteria, genes_busco)
overlaps <- pintersect(genes_bacteria[queryHits(hits)], genes_busco[subjectHits(hits)])
overlaps$with <- width(overlaps)
overlaps$with_bacteria<-width(genes_bacteria[queryHits(hits)])
overlaps$with_busco<-width(genes_busco[subjectHits(hits)])
overlaps$percentOverlap <- width(overlaps) / width(genes_bacteria[queryHits(hits)])

And I got something like:

> overlaps
GRanges object with 1 range and 5 metadata columns:
        seqnames    ranges strand |       hit      with with_bacteria with_busco    percentOverlap
           <Rle> <IRanges>  <Rle> | <logical> <integer>  <integer>  <integer>         <numeric>
  [1] scaffold_2 1550-1650      + |      TRUE       101        201        101 0.502487562189055
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths

And at the end the aim of my question should be to remove all the overlapping ranges in my genes_bacteria object so here to get:

 > genes_bacteria

            GRanges object with 30047 ranges and 0 metadata columns:
                            seqnames      ranges strand
                               <Rle>   <IRanges>  <Rle>
                  [1]     scaffold_1 1-50      +
                  [2]     scaffold_1 60-100      +
                  [3]     scaffold_1 200-350      +
                  [5]     scaffold_2 1900-2300      +
                  [6]     scaffold_5   250-255      -
              -------

As you can see, Scaffold_2 has been deleted because it overlaps. Thank you for your help.