Actually this might not be that hard.

Do a union(x, y) to merge the ranges, then use findOverlaps(x/y, union,
select="first") to get a match vector to merge the columns.


On Wed, Oct 16, 2013 at 7:39 AM, John linux-user <johnlinuxuser@yahoo.com>wrote:

> Thanks for your reply, but both match and merge functions do not solve the
> problem because the range field might be different for two objects as
> exampled below. I  made a program using Python to solve this problem but
> hopefully some one in R should write a simple function for this problem.
>
>
>   On Wednesday, October 16, 2013 10:23 AM, Michael Lawrence <
> lawrence.michael@gene.com> wrote:
>  If you just need to merge the Val from obj2 as a column in obj1, i.e.,
> there is no need to add ranges from obj2 to obj1, then it's simple using
> match(). If you need the equivalent of merge(all=TRUE), then you need to
> convert to data frames, use merge() and convert back. There is a
> merge,VRanges method that does this. Nothing for GRanges yet though.
>
>
> On Wed, Oct 16, 2013 at 7:15 AM, John linux-user <johnlinuxuser@yahoo.com>wrote:
>
> Hello everyone,
>
> I am wondering how to simply merge two GRanges objects by range field and
> add the value by additional vector. For example, I have two objects below
>
> obj1
>
> seqnames           ranges strand |       Val
>             <Rle>        <IRanges>  <Rle> | <integer>
>   [1] chr1_random [272531, 272571]      + |        88
>   [2] chr1_random [272871, 272911]      + |        45
>
> obj2
>  seqnames           ranges strand |       Val
>             <Rle>        <IRanges>  <Rle> | <integer>
>   [1] chr1_random [272531, 272581]      + |        800
>   [2] chr1_random [272850, 272911]      + |        450
>
> after merged, it should be an object as the following mergedObject and it
> would concern the differences in IRANGE data (e.g. 581 and 850 in obj2
> above were different from those of obj1, which were 571 and 871
> respectively)
>
> mergedObject
>
>  seqnames           ranges strand                 |         object2Val
> object1Val
>             <Rle>        <IRanges>  <Rle>         |         <integer>
> <integer>
>   [1] chr1_random [272531, 272581]      + |        800               88
>   [2] chr1_random [272850, 272911]      + |        450               45
>
>
>
>
> On Tuesday, October 15, 2013 12:36 PM, Lukasz [guest] <
> guest@bioconductor.org> wrote:
>
>

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