Hi,

I invoked the following command:

dist <- distanceToNearest(rt.gr, mop, ignore.strand = TRUE)

Note: rt.gr and mop are granges

I found out that NROW(dist) is one row shorter than NROW(rt.gr), meaning thate is one range in rt.gr that does not have a corresponding nearest range in mop. How do I find the missing row equivalent in rt.gr? Possibly did not return a value? I have checked ranges(rt.gr) for non-numeric values and did not find any.

Thanks

You shouldn't expect that the length of dist will be the same as the length as your rt.gr object. Also, by 'self-contained' example, I meant something that other people could run. Just showing your code is not self-contained because I don't have your data. But here is an example.

## run this first
> example(distanceToNearest) 
> query
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        A         1      *
  [2]        B         5      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> subject
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        A      6-10      *
  [2]        A      5-10      *
  [3]        A     13-15      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

## this will return a Hits object that conforms to the 'subject' GRanges object
> distanceToNearest(subject, query)
Hits object with 3 hits and 1 metadata column:
      queryHits subjectHits |  distance
      <integer>   <integer> | <integer>
  [1]         1           1 |         4
  [2]         2           1 |         3
  [3]         3           1 |        11
  -------
  queryLength: 3 / subjectLength: 2

## this will return a Hits object that DOES NOT conform to the 'query' GRanges object.
> distanceToNearest(query,subject)
Hits object with 1 hit and 1 metadata column:
      queryHits subjectHits |  distance
      <integer>   <integer> | <integer>
  [1]         1           2 |         3
  -------
  queryLength: 2 / subjectLength: 3