[BioC] nearest() for GRanges
Valerie Obenchain
vobencha at fhcrc.org
Fri Jun 22 23:00:32 CEST 2012
On 06/20/2012 05:20 PM, Cook, Malcolm wrote:
> Hi Valerie,
>
> Very glad you found and fixed the root cause.
>
> I don't know the overhead it would take for you, but, this being a
> regression, might you consider fixing in Bioconductor 2.10 as, say
> GenomicRanges_1.8.
>
Yes, I will fix this in release too. If not today then first thing next
week.
Valerie
> Thanks for your consideration,
>
> Malcolm
>
> On 6/20/12 3:13 PM, "Valerie Obenchain"<vobencha at fhcrc.org> wrote:
>
>> Hi Oleg, Malcom,
>>
>> Thanks for the bug report. This is now fixed in devel 1.9.28. Over the
>> past months we've done an overhaul of the precede/follow code in devel.
>> The new nearest method is based on the new precede and follow and is
>> documented at
>>
>> ?'nearest,GenomicRanges,GenomicRanges-method'
>>
>> Let me know if you run into problems.
>>
>> Valerie
>>
>>
>>
>> On 06/18/2012 02:25 PM, Cook, Malcolm wrote:
>>> Martin, Oleg, Val, all,
>>>
>>> I too have script logic that benefitted from and depends upon what the
>>> behavior of nearest,GenomicRanges,missing as reported by Oleg.
>>>
>>> Thanks for the unit tests Martin.
>>>
>>> If it helps in sleuthing, in my hands, the 3rd test used to pass (if my
>>> memory serves), but does not pass now, as the attached transcript shows.
>>>
>>> Hoping it helps find a speedy resolution to this issue,
>>>
>>> ~ Malcolm Cook
>>>
>>>
>>>
>>>> r<- IRanges(c(1,5,10), c(2,7,12))
>>>> g<- GRanges("chr1", r, "+")
>>>> checkEquals(precede(r), precede(g))
>>> [1] TRUE
>>>> checkEquals(follow(r), follow(g))
>>> [1] TRUE
>>>> try(checkEquals(nearest(r), nearest(g)))
>>> Error in checkEquals(nearest(r), nearest(g)) :
>>> Mean relative difference: 0.6
>>>
>>>
>>>> sessionInfo()
>>> R version 2.15.0 (2012-03-30)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] tools splines parallel stats graphics grDevices utils
>>> datasets methods base
>>>
>>> other attached packages:
>>> [1] RUnit_0.4.26 log4r_0.1-4 vwr_0.1
>>> RecordLinkage_0.4-1 ffbase_0.5 ff_2.2-7
>>> bit_1.1-8 evd_2.2-6 ipred_0.8-13
>>> prodlim_1.3.1 KernSmooth_2.23-7 nnet_7.3-1
>>> survival_2.36-14 mlbench_2.1-0 MASS_7.3-18
>>> ada_2.0-2 rpart_3.1-53 e1071_1.6
>>> class_7.3-3 XLConnect_0.1-9 XLConnectJars_0.1-4
>>> rJava_0.9-3 latticeExtra_0.6-19 RColorBrewer_1.0-5
>>> lattice_0.20-6 doMC_1.2.5 multicore_0.1-7
>>> [28] BSgenome_1.24.0 rtracklayer_1.16.1 Rsamtools_1.8.5
>>> Biostrings_2.24.1 GenomicFeatures_1.8.1 AnnotationDbi_1.18.1
>>> GenomicRanges_1.8.6 IRanges_1.14.3 Biobase_2.16.0
>>> BiocGenerics_0.2.0 data.table_1.8.0 compare_0.2-3
>>> svUnit_0.7-10 doParallel_1.0.1 iterators_1.0.6
>>> foreach_1.4.0 ggplot2_0.9.1 sqldf_0.4-6.4
>>> RSQLite.extfuns_0.0.1 RSQLite_0.11.1 chron_2.3-42
>>> gsubfn_0.6-3 proto_0.3-9.2 DBI_0.2-5
>>> functional_0.1 reshape_0.8.4 plyr_1.7.1
>>> [55] stringr_0.6 gtools_2.6.2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.12.0 bitops_1.0-4.1
>>> codetools_0.2-8 colorspace_1.1-1 compiler_2.15.0 dichromat_1.2-4
>>> digest_0.5.2 grid_2.15.0 labeling_0.1 memoise_0.1
>>> munsell_0.3 reshape2_1.2.1 scales_0.2.1 stats4_2.15.0
>>> tcltk_2.15.0 zlibbioc_1.2.0
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 6/18/12 2:39 PM, "Martin Morgan"<mtmorgan at fhcrc.org> wrote:
>>>
>>>> Hi Oleg --
>>>>
>>>> On 06/17/2012 11:11 PM, Oleg Mayba wrote:
>>>>> Hi,
>>>>>
>>>>> I just noticed that a piece of logic I was relying on with GRanges
>>>>> before
>>>>> does not seem to work anymore. Namely, I expect the behavior of
>>>>> nearest()
>>>>> with a single GRanges object as an argument to be the same as that of
>>>>> IRanges (example below), but it's not anymore. I expect nearest(GR1)
>>>>> NOT
>>>>> to behave trivially but to return the closest range OTHER than the
>>>>> range
>>>>> itself. I could swear that was the case before, but isn't any longer:
>>>> I think you're right that there is an inconsistency here; Val will
>>>> likely help clarify in a day or so. My two cents...
>>>>
>>>> I think, certainly, that GRanges on a single chromosome on the "+"
>>>> strand should behave like an IRanges
>>>>
>>>> library(GenomicRanges)
>>>> library(RUnit)
>>>>
>>>> r<- IRanges(c(1,5,10), c(2,7,12))
>>>> g<- GRanges("chr1", r, "+")
>>>>
>>>> ## first two ok, third should work but fails
>>>> checkEquals(precede(r), precede(g))
>>>> checkEquals(follow(r), follow(g))
>>>> try(checkEquals(nearest(r), nearest(g)))
>>>>
>>>> Also, on the "-" strand I think we're expecting
>>>>
>>>> g<- GRanges("chr1", r, "-")
>>>>
>>>> ## first two ok, third should work but fails
>>>> checkEquals(follow(r), precede(g))
>>>> checkEquals(precede(r), follow(g))
>>>> try(checkEquals(nearest(r), nearest(g)))
>>>>
>>>> For "*" (which was your example) I think the situation is (a) different
>>>> in devel than in release; and (b) not so clear. In devel, "*" is (from
>>>> method?"nearest,GenomicRanges,missing") "x on '*' strand can match to
>>>> ranges on any of ''+'', ''-'' or ''*''" and in particular I think these
>>>> are always true:
>>>>
>>>> checkEquals(precede(g), follow(g))
>>>> checkEquals(nearest(r), follow(g))
>>>>
>>>> I would also expect
>>>>
>>>> try(checkEquals(nearest(g), follow(g)))
>>>>
>>>> though this seems not to be the case. In 'release', "*" is coereced and
>>>> behaves as if on the "+" strand (I think).
>>>>
>>>> Martin
>>>>
>>>>>> z=IRanges(start=c(1,5,10), end=c(2,7,12))
>>>>>> z
>>>>> IRanges of length 3
>>>>> start end width
>>>>> [1] 1 2 2
>>>>> [2] 5 7 3
>>>>> [3] 10 12 3
>>>>>> nearest(z)
>>>>> [1] 2 1 2
>>>>>> z=GRanges(seqnames=rep('chr1',3),ranges=IRanges(start=c(1,5,10),
>>>>> end=c(2,7,12)))
>>>>>> z
>>>>> GRanges with 3 ranges and 0 elementMetadata cols:
>>>>> seqnames ranges strand
>>>>> <Rle> <IRanges> <Rle>
>>>>> [1] chr1 [ 1, 2] *
>>>>> [2] chr1 [ 5, 7] *
>>>>> [3] chr1 [10, 12] *
>>>>> ---
>>>>> seqlengths:
>>>>> chr1
>>>>> NA
>>>>>> nearest(z)
>>>>> [1] 1 2 3
>>>>>> sessionInfo()
>>>>> R version 2.15.0 (2012-03-30)
>>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>>
>>>>> locale:
>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>>>> [7] LC_PAPER=C LC_NAME=C
>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>>
>>>>> attached base packages:
>>>>> [1] datasets utils grDevices graphics stats methods base
>>>>>
>>>>> other attached packages:
>>>>> [1] GenomicRanges_1.8.6 IRanges_1.14.3 BiocGenerics_0.2.0
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] stats4_2.15.0
>>>>>
>>>>>
>>>>> I want the IRanges behavior and not what seems currently to be the
>>>>> GRanges
>>>>> behavior, since I have some code that depends on it. Is there a quick
>>>>> way
>>>>> to make nearest() do that for me again?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Oleg.
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
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>>>> --
>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N.
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>>>>
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>>>> Phone: (206) 667-2793
>>>>
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