[BioC] Bug in set operations over IRanges objects with non-NULL elementMetadata()

[Steve Lianoglou]

Thanks for taking care of that, Michael.

-steve

On Sat, Oct 23, 2010 at 11:01 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> These issues should now be resolved as of 1.9.1. Sure there's a lot more out
> there.
>
> Michael
>
> On Fri, Oct 15, 2010 at 6:57 AM, Michael Lawrence <michafla at gene.com> wrote:
>>
>> I believe the convention up till now has been to quietly drop the
>> metadata, and that makes sense to me.
>>
>> I can work on fixing some of these methods. I'm sure there are such issues
>> all over IRanges, as element metadata was incorporated fairly late in the
>> game.
>>
>> Michael
>>
>> On Thu, Oct 14, 2010 at 7:43 PM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com> wrote:
>>>
>>> Actually, I have a vague feeling of this maybe coming up before (maybe
>>> even from me(?)).
>>>
>>> I understand that it's not clear what to do with the DataFrame
>>> values() when merging/intersecting/union/etc. two IRanges, so I would
>>> imagine either:
>>>
>>> (i) dropping the values() from both might be fine (w/ a warning()?);
>>> or if you really think this should be an error no matter what
>>>
>>> (ii) at least give a better error message in this situation so the
>>> user can smoke out what's wrong and fix.
>>>
>>> Thanks,
>>> -steve
>>>
>>>
>>> On Thu, Oct 14, 2010 at 9:55 PM, Steve Lianoglou
>>> <mailinglist.honeypot at gmail.com> wrote:
>>> > Hi,
>>> >
>>> > Subject says it all. Here's an example:
>>> >
>>> > R> library(IRanges)
>>> > R> i1 <- IRanges(1, 10)
>>> > R> i2 <- IRanges(c(1, 15), width=5)
>>> > R> i3 <- i2
>>> > R> values(i3) <- DataFrame(score=1:2)
>>> >
>>> > R> union(i1, i2)
>>> > IRanges of length 2
>>> >    start end width
>>> > [1]     1  10    10
>>> > [2]    15  19     5
>>> >
>>> > R> union(i1, i3)
>>> > Error in reduce(c(x0, y), drop.empty.ranges = TRUE) :
>>> >  error in evaluating the argument 'x' in selecting a method for
>>> > function 'reduce'
>>> >
>>> > R> setdiff(i1, i2)
>>> > IRanges of length 1
>>> >    start end width
>>> > [1]     6  10     5
>>> >
>>> > R> setdiff(i1, i3)
>>> > Error in gaps(union(gaps(x, start = start, end = end), y), start =
>>> > start,  :
>>> >  error in evaluating the argument 'x' in selecting a method for
>>> > function 'gaps'
>>> >
>>> > R> sessionInfo()
>>> > R version 2.12.0 beta (2010-09-30 r53084)
>>> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>> >
>>> > locale:
>>> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>> >
>>> > attached base packages:
>>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>>> >
>>> > other attached packages:
>>> > [1] GenomicRanges_1.1.36 IRanges_1.7.39
>>> >
>>> > -steve
>>> >
>>> > --
>>> > Steve Lianoglou
>>> > Graduate Student: Computational Systems Biology
>>> >  | Memorial Sloan-Kettering Cancer Center
>>> >  | Weill Medical College of Cornell University
>>> > Contact Info: http://cbio.mskcc.org/~lianos/contact
>>> >
>>>
>>>
>>>
>>> --
>>> Steve Lianoglou
>>> Graduate Student: Computational Systems Biology
>>>  | Memorial Sloan-Kettering Cancer Center
>>>  | Weill Medical College of Cornell University
>>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>>
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>>
>
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact