[R] how to merge GRange object?

[Martin Morgan]

On 10/16/2013 06:32 AM, John linux-user 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
>

Hi -- GRanges is from a Bioconductor package, so please ask on the Bioconductor 
mailing list

   http://bioconductor.org/help/mailing-list/

I think you might do hits = findOverlaps(obj1, obj2) to get indexes of 
overlapping ranges, then pmin(obj1[queryHits(obj1)], obj2[subjectHits(obj2)]) 
and pmax() to get start and end coordinates, and construct a new GRanges from 
those. If you provide an easily reproducile example (e.g., constructing some 
sample GRanges objects 'by hand' using GRanges()) and post to the Bioconductor 
mailing list you'll likely get a complete answer.

Martin

> 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 Wednesday, October 16, 2013 8:31 AM, Terry Therneau <therneau at mayo.edu> wrote:
>
>
>
> On 10/16/2013 05:00 AM, r-help-request at r-project.org wrote:
>> Hello,
>>
>> I'm trying to use coxph() function to fit a very simple Cox proportional
>> hazards regression model (only one covariate) but the parameter space is
>> restricted to an open set (0, 1). Can I still obtain a valid estimate by
>> using coxph function in this scenario? If yes, how? Any suggestion would be
>> greatly appreciated. Thanks!!!
>
> Easily:
>      1.  Fit the unrestricted model.  If the solution is in 0-1 you are done.
>      2.  If it is outside, fix the coefficient.  Say that the solution is 1.73, then the
> optimal solution under contraint is 1.
>          Redo the fit adding the paramters  "init=1, iter=0".  This forces the program to
> give the loglik and etc for the fixed coefficient of 1.0.
>
> Terry Therneau
>
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>
>
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>


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