Dear All
I have GRanges objects of transcript information (subject) & for regions of
interest (query).
Top lines of (subject):
     seqnames                 ranges strand   |     tx_id            tx_name
             <Rle>              <IRanges>  <Rle>   | <integer>
<character>
      [1]        1          [5473, 16844]      +   |         1
ENSRNOT00000044270
      [2]        1          [5526, 16968]      +   |         2
ENSRNOT00000049921
      [3]        1          [5526, 16968]      +   |         3
ENSRNOT00000051735
      [4]        1          [5598, 13520]      +   |         4
ENSRNOT00000034630
      [5]        1          [8268, 16850]      +   |         5
ENSRNOT00000044505
      [6]        1          [8316, 17577]      +   |         6
ENSRNOT00000042693
      [7]        1          [8884, 16850]      +   |         7
ENSRNOT00000044187
      [8]        1          [8956,  9955]      +   |         8
ENSRNOT00000041082
      [9]        1          [9055, 17351]      +   |         9
ENSRNOT00000050254

Top lines of (query):
        seqnames                 ranges strand
            <Rle>              <IRanges>  <Rle>
     [1]       10 [ 37958164,  37958165]      +   |
     [2]        7 [ 46598224,  46598225]      -   |
     [3]        1 [  9627018,   9627019]      -   |
     [4]        9 [ 10158183,  10158184]      +   |
     [5]        2 [185436985, 185436986]      +   |
     [6]        8 [ 93638247,  93638248]      -   |
     [7]        7 [ 68559015,  68559016]      -   |
     [8]       12 [ 10978744,  10978745]      +   |
     [9]       17 [ 33460790,  33460791]      -   |

and am using the precede command to find the preceeding transcripts to my
regions of interest

output<-precede(query, subject, ignore.strand=FALSE)

I am aware that the object called "output" is of class integer with the row
names of "subject" which represent the preceding hits for "query", but I
have so far been unable to use these row names to end up with a granges
object with the name of the preceding transcripts as metadata in a granges
object containing the ranges from "query" i.e something that would look
like:
[1]       10 [ 37958164,  37958165]      +   |ENSRNOT00000044270

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