Hi
I am very much a learner in R in general & GenomicRanges in general
I am struggling to find documentation to help me get my head around
distanceToNearest in GenomicRanges
If I have a GRanges object:

GRanges with 6 ranges and 4 metadata columns:
      seqnames                 ranges strand |
         <Rle>              <IRanges>  <Rle> |
  [1]       10 [ 96723746,  96723747]      - |
  [2]        7 [ 13641170,  13641171]      + |
  [3]       16 [ 17772801,  17772802]      - |
  [4]        3 [ 88173502,  88173503]      - |
  [5]       13 [106979682, 106979683]      + |
  [6]        9 [104393139, 104393140]      + |

(You will notice that all the regions are only dinucleotides & I have
removed the metadata )

I have a 2nd GRanges object which is ensembl rat transcripts as below:
39549 ranges and 2 metadata columns:
          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


If I invoke:
xx<-distanceToNearest(diff.cpgs.gr, rat.transcripts, ignore.strand=F)

xx
DataFrame with 1133 rows and 3 columns
     queryHits subjectHits  distance
     <integer>   <integer> <integer>
1            1        7752         0
2            2       32166     11946
3            3       14678     25377
4            4       24286     66747
5            5       10609     34242
6            6       37076    122683
7            7       35184         0
8            8       34180     45561
9            9       19351     50156
...        ...         ...       ...
etc

I am uncertain how I would then use the xx output to gain information (i.e.
tx_id, tx_name) about the feature which the function has identified as
nearest?
I would be happy to supply any more info as required
Tom

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