Hi
In the following example, I am trying to use 'reduce()' function to reduce
the genomic intervals and find intervals corresponding to  'Gene'. It is
behaving as it is desired. However the output of the reduce just give the
intervals (I am losing the 'Gene' metadata).
Is there a way to retain 'Gene' metadata.


>       gr <- GRanges(+                     seqnames = Rle(c("chr1", "chr2", "chr2"), c(6, 2,2)), +                     ranges = IRanges(c(1:6, 1:2, 10:11) , end = c(7:12, 5,9, 18:19 )), +                     strand = Rle(strand(c("-", "+", "-", "*")),c(3, 3, 2,2)), +                     transcript  = head(letters, 10),+                     Gene = c(rep("xxx",3), rep("yyy",3), rep("zzz",2), rep("www",2)) +                     )>       grGRanges with 10 ranges and 2 elementMetadata values:
       seqnames    ranges strand |  transcript        Gene
          <Rle> <IRanges>  <Rle> | <character> <character>
   [1]     chr1  [ 1,  7]      - |           a         xxx
   [2]     chr1  [ 2,  8]      - |           b         xxx
   [3]     chr1  [ 3,  9]      - |           c         xxx
   [4]     chr1  [ 4, 10]      + |           d         yyy
   [5]     chr1  [ 5, 11]      + |           e         yyy
   [6]     chr1  [ 6, 12]      + |           f         yyy
   [7]     chr2  [ 1,  5]      - |           g         zzz
   [8]     chr2  [ 2,  9]      - |           h         zzz
   [9]     chr2  [10, 18]      * |           i         www
  [10]     chr2  [11, 19]      * |           j         www
  ---
  seqlengths:
   chr1 chr2
     NA   NA>       x = reduce(gr)>       xGRanges with 4 ranges and 0
elementMetadata values:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  [ 4, 12]      +
  [2]     chr1  [ 1,  9]      -
  [3]     chr2  [ 1,  9]      -
  [4]     chr2  [10, 19]      *
  ---
  seqlengths:
   chr1 chr2
     NA   NA

>


Thanks


Fahim

-- 
-------------------------------
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA

	[[alternative HTML version deleted]]

