Hi Steve, Michael and Malcolm,

Thanks very much for your suggestions.

I'd need to think about how to deal with these overlapping signals as well
before I give Steve's suggestion a go!

Thanks again for your kind advice and guidance!

Jeremy

On Sat, Mar 22, 2014 at 6:02 AM, Michael Lawrence <lawrence.michael@gene.com
> wrote:

> It could be that Steve's suggestion solves your problems, but you might
> want to clarify how you want to merge the data. It looks like
> gsm97tf.ranges has internal overlaps (e.g., the first two ranges), so it's
> not obvious which signal should be assigned to the intersection.
>
>
> On Fri, Mar 21, 2014 at 1:50 PM, Jeremy Ng <jeremy.ng.wk1990@gmail.com>wrote:
>
>> Hi there,
>>
>> I'm relatively new to the GRanges class of objects, and have some
>> questions; and hopefully, I'd be able to better understand what's going on
>> here.
>>
>> I have 2 Granges objects, which are data from GEO. I want to find where
>> the
>> overlap, and then after that, the signals from each set. Here's what I
>> have
>> so far:
>>
>> >gsm97tf.ranges
>> GRanges with 171378 ranges and 1 metadata column:
>>            seqnames                 ranges strand   |    signal
>>               <Rle>              <IRanges>  <Rle>   | <numeric>
>>        [1]    chr10   [54828986, 54829035]      +   |      0.79
>>        [2]    chr10   [54829024, 54829073]      +   |      0.05
>>        [3]    chr10   [54829176, 54829225]      +   |      0.04
>>        [4]    chr10   [54829746, 54829795]      +   |      0.15
>>        [5]    chr10   [54829898, 54829947]      +   |      0.24
>>        ...      ...                    ...    ... ...       ...
>>   > gsm94tf.ranges
>> GRanges with 171249 ranges and 1 metadata column:
>>            seqnames                 ranges strand   |    signal
>>               <Rle>              <IRanges>  <Rle>   | <numeric>
>>        [1]    chr10   [54828834, 54828883]      +   |      0.65
>>        [2]    chr10   [54828986, 54829035]      +   |      0.73
>>        [3]    chr10   [54829024, 54829073]      +   |      0.33
>>        [4]    chr10   [54829138, 54829187]      +   |      0.02
>>        [5]    chr10   [54829176, 54829225]      +   |      0.02
>>
>> In order to find the regions of the genome where both sets overlap, I use
>> the following:
>>
>> overlaps<-intersect(gsm94tf.ranges,gsm97tf.ranges)
>>
>> This will give me a GRanges object containing the coordinates where both
>> sets intersect. The result looks like this:
>> >overlaps
>> GRanges with 72012 ranges and 0 metadata columns:
>>           seqnames                 ranges strand
>>              <Rle>              <IRanges>  <Rle>
>>       [1]     chr1 [148374757, 148374806]      +
>>       [2]     chr1 [148374833, 148374996]      +
>>       [3]     chr1 [148375061, 148375148]      +
>>       [4]     chr1 [148375821, 148375870]      +
>>       [5]     chr1 [148376087, 148376212]      +
>>
>> My next question seems pretty trivial, but I'm stuck on what to go on
>> next.
>> I want to map back the overlaps to the original sets, to find their signal
>> values. I was wondering, how do I do this?
>>
>> Sorry if this question is pretty simple - I'm trying to get a better
>> handle
>> of the GRanges classes!
>>
>> Thanks for any pointers!
>>
>> Jeremy
>>
>>         [[alternative HTML version deleted]]
>>
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>
>

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