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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>
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