I'm interested in finding the nearest neighbor to each gene within a list.

> distanceToNearest(x = sub.gr, subject = sub.gr)
Hits object with 5803 hits and 1 metadata column:
         queryHits subjectHits |  distance
         <integer>   <integer> | <integer>
     [1]         1           1 |         0
     [2]         2           2 |         0
     [3]         3           3 |         0
     [4]         4           4 |         0
     [5]         5           5 |         0
     ...       ...         ... .       ...
  [5799]      5799        5799 |         0
  [5800]      5800        5800 |         0
  [5801]      5801        5800 |         0
  [5802]      5802        5802 |         0
  [5803]      5803        5802 |         0
  -------
  queryLength: 5803 / subjectLength: 5803

It effectively finds itself in the list and so distance = 0. Is there a way to find the second Nearest?

SOLUTION

> distanceToNearest(x = sub.gr)
Hits object with 5301 hits and 1 metadata column:
         queryHits subjectHits |  distance
         <integer>   <integer> | <integer>
     [1]         1           2 |        38
     [2]         2           1 |        38
     [3]         3           4 |      2613
     [4]         4           5 |       297
     [5]         5           4 |       297
     ...       ...         ... .       ...
  [5297]      5799        5800 |        52
  [5298]      5800        5801 |         0
  [5299]      5801        5800 |         0
  [5300]      5802        5803 |         0
  [5301]      5803        5802 |         0
  -------
  queryLength: 5803 / subjectLength: 5803