Hi Valerie,

Thanks much for the fix!

Best,

--t


On Thu, Feb 14, 2013 at 11:39 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> Hi Tim,
>
> Thanks for reporting this. There was a typo in the method called for
> 3UTR's in the AllVariants() code. Now fixed in 1.5.38 and 1.4.9.
>
> library(Homo.sapiens)
> library(VariantAnnotation)
> library(TxDb.Hsapiens.UCSC.**hg19.knownGene)
> txdb <- TxDb.Hsapiens.UCSC.hg19.**knownGene
>
> site <- GRanges(c('chr1'), IRanges(start=36521401, width=1))
> EIF2C3 <- unlist(mget('EIF2C3', org.Hs.egSYMBOL2EG))
>
> all <- locateVariants(site, txdb, AllVariants())
> three <- locateVariants(site, txdb, ThreeUTRVariants())
>
> > identical(all, three)
> [1] TRUE
>
>
> Valerie
>
>
>
>
>
> On 02/13/2013 10:19 PM, Tim Triche, Jr. wrote:
>
>> Somehow I omitted a line... this should go immediately after
>> library(VariantAnnotation), i.e.
>>
>>
>> library(Homo.sapiens)
>> library(VariantAnnotation)
>>
>> ## this following line is the one that went missing
>> EIF2C3 <- unlist(mget('EIF2C3', org.Hs.egSYMBOL2EG))
>>
>> EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1))
>> EIF2C3.site %over%
>> transcriptsBy(TxDb.Hsapiens.**UCSC.hg19.knownGene)[[EIF2C3]]
>>
>> ## ...the rest is as before
>>
>>
>> On Wed, Feb 13, 2013 at 5:09 PM, Tim Triche, Jr. <tim.triche@gmail.com
>> >wrote:
>>
>>  I was reannotating some discriminating loci today and found this odd case
>>> -- a site is in the 3' UTR of two transcripts for a gene, and
>>> threeUTRVariants() finds it, but AllVariants() does not.
>>>
>>> Code to reproduce the result at an example locus:
>>>
>>> packageVersion('**VariantAnnotation')
>>> ## [1] '1.5.36'
>>> packageVersion('Homo.sapiens')
>>> ## [1] '1.0.0'
>>>
>>> ## test case for bioc-list:
>>> library(Homo.sapiens)
>>> library(VariantAnnotation)
>>> EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1))
>>> EIF2C3.site %over%
>>> transcriptsBy(TxDb.Hsapiens.**UCSC.hg19.knownGene)[[EIF2C3]]
>>> ## TRUE
>>>
>>> allVars <- locateVariants(EIF2C3.site,
>>>                            TxDb.Hsapiens.UCSC.hg19.**knownGene,
>>>                            AllVariants())
>>> length(allVars)
>>> ## 0
>>>
>>> threePrimeVars <- locateVariants(EIF2C3.site,
>>>                                   TxDb.Hsapiens.UCSC.hg19.**knownGene,
>>>                                   ThreeUTRVariants())
>>> length(threePrimeVars)
>>> ## 2
>>>
>>> Why aren't the 3' UTR matches included in the AllVariants() results?
>>> That doesn't seem like the expected behavior, at least not to me.
>>>
>>>
>>>
>>> R> sessionInfo()
>>> R Under development (unstable) (2013-02-13 r61937)
>>> 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] parallel  stats     graphics  grDevices datasets  utils     methods
>>> [8] base
>>>
>>> other attached packages:
>>>   [1] FDb.InfiniumMethylation.hg19_**1.0.6
>>>   [2] BSgenome.Hsapiens.UCSC.hg19_1.**3.19
>>>   [3] BSgenome_1.27.1
>>>   [4] Homo.sapiens_1.0.0
>>>   [5] TxDb.Hsapiens.UCSC.hg19.**knownGene_2.8.0
>>>    [6] org.Hs.eg.db_2.8.0
>>>   [7] GO.db_2.8.0
>>>   [8] RSQLite_0.11.2
>>>   [9] DBI_0.2-5
>>> [10] OrganismDbi_1.1.13
>>> [11] VariantAnnotation_1.5.36
>>> [12] Rsamtools_1.11.16
>>> [13] Biostrings_2.27.11
>>> [14] GenomicFeatures_1.11.8
>>>   [15] AnnotationDbi_1.21.10
>>> [16] Biobase_2.19.2
>>> [17] chromophobe_0.50
>>> [18] pheatmap_0.7.4
>>> [19] ggplot2_0.9.3
>>> [20] reshape2_1.2.2
>>> [21] GenomicRanges_1.11.29
>>> [22] IRanges_1.17.31
>>> [23] BiocGenerics_0.5.6
>>>   [24] BiocInstaller_1.9.6
>>> [25] gtools_2.7.0
>>> [26] devtools_1.1
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] biomaRt_2.15.0     bitops_1.0-5       colorspace_1.2-1
>>> dichromat_2.0-0
>>>   [5] digest_0.6.2       evaluate_0.4.3     graph_1.37.5       grid_3.0.0
>>>
>>>   [9] gtable_0.1.2       httr_0.2           labeling_0.1
>>> lattice_0.20-13
>>> [13] MASS_7.3-23        Matrix_1.0-10      memoise_0.1        munsell_0.4
>>>
>>> [17] plyr_1.8           proto_0.3-10       RBGL_1.35.0
>>>   RColorBrewer_1.0-5
>>> [21] RCurl_1.95-3       rtracklayer_1.19.9 scales_0.2.3
>>> stats4_3.0.0
>>>
>>> [25] stringr_0.6.2      tcltk_3.0.0        tools_3.0.0        whisker_0.1
>>>
>>> [29] XML_3.95-0.1       zlibbioc_1.5.0
>>>
>>>
>>> --
>>> *A model is a lie that helps you see the truth.*
>>> *
>>> *
>>> Howard Skipper<http://cancerres.**aacrjournals.org/content/31/9/**
>>> 1173.full.pdf<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>>> >
>>>
>>>
>>
>>
>>
>


-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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