[BioC] query and subject hits in findOverlaps through different space names

Martin Morgan mtmorgan at fhcrc.org
Wed Apr 14 00:14:08 CEST 2010


On 04/13/2010 02:16 PM, Robert Castelo wrote:
> thanks Michael for fixing this quickly, one minor detail, i've noticed
> that the version
> number of the IRanges code i've checked out with the fix from the svn
> repository is
> 1.5.76 which is the same that showed up in the sessionInfo() below
> reporting the bug.
> maybe it is ok like this, but just wanted to point it out in case that
> it should be different
> for the automagic update.packages() thingy.

Hi Robert -- that must have been an oversight on Michael's part and I've
bumped the version, thanks. Martin

> 
> cheers,
> robert.
> 
> 
> On 4/13/10 5:13 PM, Michael Lawrence wrote:
>> Yes this has been fixed.
>>
>> On Tue, Apr 13, 2010 at 7:24 AM, James W. MacDonald
>> <jmacdon at med.umich.edu>wrote:
>>
>>   
>>> Has this been fixed in svn?
>>>
>>> Michael Lawrence wrote:
>>>
>>>     
>>>> On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo<robert.castelo at upf.edu
>>>>       
>>>>> wrote:
>>>>>          
>>>>   dear list and, particularly, IRanges developers,
>>>>       
>>>>> i've noticed a change shown below in the functionality of the
>>>>> findOverlap function from the IRanges package from the current BioC
>>>>> release version 2.10 to the current BioC devel (about to become
>>>>> release)
>>>>> version 2.11 (i've checked-out the latest IRanges version at the svn
>>>>> repository).
>>>>>
>>>>> this change seems to alter the way in which findOverlaps() return the
>>>>> hits. in the current release findOverlaps() was returning the index of
>>>>> the hits with respect to the entire RangedData object while in the
>>>>> current devel version it does it with respect to the corresponding
>>>>> space. is this an intended change or is it a bug? (i was happier with
>>>>> the behavior of the release..)
>>>>>
>>>>>
>>>>>   It's a bug. Dimensions got switched around in RangesMatching, which
>>>>>          
>>>> confused
>>>> RangesMatchingList. It's been broken since 2/26/10, in case anyone
>>>> wants
>>>> to
>>>> re-run their scripts.
>>>>
>>>> Thanks a lot for catching this,
>>>>
>>>> Michael
>>>>
>>>>
>>>>   thanks!
>>>>       
>>>>> robert.
>>>>>
>>>>> =========================current release 2.10==================
>>>>> suppressPackageStartupMessages(library(IRanges))
>>>>>
>>>>> x<- RangedData(IRanges(start=c(1,6), end=c(5,10)),
>>>>>                        space=c("chr1","chr2"))
>>>>> x
>>>>> RangedData with 2 rows and 0 value columns across 2 spaces
>>>>>        space    ranges |
>>>>>   <character>  <IRanges>  |
>>>>> 1        chr1   [1,  5] |
>>>>> 2        chr2   [6, 10] |
>>>>>
>>>>> y<- RangedData(IRanges(start=8, end=10),
>>>>>                        space="chr2")
>>>>> y
>>>>> RangedData with 1 row and 0 value columns across 1 space
>>>>>        space    ranges |
>>>>>   <character>  <IRanges>  |
>>>>> 1        chr2   [8, 10] |
>>>>>
>>>>> as.matrix(findOverlaps(x, y))
>>>>>     query subject
>>>>> [1,]     2       1
>>>>> sessionInfo()
>>>>> R version 2.10.1 (2009-12-14)
>>>>> x86_64-unknown-linux-gnu
>>>>>
>>>>> locale:
>>>>> [1] C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods
>>>>> base
>>>>>
>>>>> other attached packages:
>>>>> [1] IRanges_1.4.14
>>>>> ===============================================================
>>>>>
>>>>> ========================current devel 2.11=====================
>>>>> suppressPackageStartupMessages(library(IRanges))
>>>>>
>>>>> x<- RangedData(IRanges(start=c(1,6), end=c(5,10)),
>>>>>                        space=c("chr1","chr2"))
>>>>> x
>>>>> RangedData with 2 rows and 0 value columns across 2 spaces
>>>>>        space    ranges |
>>>>>   <character>  <IRanges>  |
>>>>> 1        chr1   [1,  5] |
>>>>> 2        chr2   [6, 10] |
>>>>> y<- RangedData(IRanges(start=8, end=10),
>>>>>                        space="chr2")
>>>>> y
>>>>> RangedData with 1 row and 0 value columns across 1 space
>>>>>        space    ranges |
>>>>>   <character>  <IRanges>  |
>>>>> 1        chr2   [8, 10] |
>>>>> as.matrix(findOverlaps(x, y))
>>>>>     query subject
>>>>> [1,]     1       1
>>>>> R version 2.11.0 Under development (unstable) (2010-02-25 r51180)
>>>>> x86_64-unknown-linux-gnu
>>>>>
>>>>> locale:
>>>>> [1] C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods
>>>>> base
>>>>>
>>>>> other attached packages:
>>>>> [1] IRanges_1.5.76
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>
>>>>>          
>>>>         [[alternative HTML version deleted]]
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>        
>>> -- 
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> Douglas Lab
>>> University of Michigan
>>> Department of Human Genetics
>>> 5912 Buhl
>>> 1241 E. Catherine St.
>>> Ann Arbor MI 48109-5618
>>> 734-615-7826
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and should
>>> not be
>>> used for urgent or sensitive issues
>>>
>>>      
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



More information about the Bioconductor mailing list