Michael and Steve,

Thank you both for your input! I will use with.mapping then.

Best regards,

Julie


On 8/7/13 2:39 PM, "Michael Lawrence" <lawrence.michael@gene.com> wrote:

As Steve said, there's no way to do this in general. However, there is a facility via the argument "with.mapping". If it is TRUE, the function will return a mapping to the original ranges, and then the merging is up to you.


On Wed, Aug 7, 2013 at 11:29 AM, Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu> wrote:
Hi,

The reduce function is very useful for joining neighboring ranges. However, the score information is lost after applying reduce. Is it possible to retain the score information after applying reduce?

Here is an example.

library(GenomicRanges)

rd <- RangedData(
      RangesList(
           chrA=IRanges(start=c(1, 4, 6), width=c(3, 2, 4)),
           chrB=IRanges(start=c(1, 3, 6), width=c(3, 3, 4))),
        score=c(2, 7, 3, 1, 1, 1))
rd
RangedData with 6 rows and 1 value column across 2 spaces
     space    ranges |     score
  <factor> <IRanges> | <numeric>
1     chrA    [1, 3] |         2
2     chrA    [4, 5] |         7
3     chrA    [6, 9] |         3
4     chrB    [1, 3] |         1
5     chrB    [3, 5] |         1
6     chrB    [6, 9] |         1

reduce(rd, min.gap=1)
RangedData with 2 rows and 0 value columns across 2 spaces
     space    ranges |
  <factor> <IRanges> |
1     chrA    [1, 9] |
2     chrB    [1, 9] |

Please note that score column is missing after applying reduce. The following is with score information.
  space    ranges | score
  <factor> <IRanges> |  <numeric>
1     chrA    [1, 9] |  12
2     chrB    [1, 9] |  3

Many thanks!

Best regards,

Julie


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