[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
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>>
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>>>>
>>>>
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>>>>
>>> --
>>> 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
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>>> **********************************************************
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>>>
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>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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