[BioC] more stupid *Ranges questions...

[Hervé Pagès]

Hi Tim,

See this email from the UCSC people for why not all UCSC Genes IDs
are mapped to an Entrez Gene ID:

   https://lists.soe.ucsc.edu/pipermail/genome/2011-April/025784.html

HTH,
H.


On 11-09-18 10:52 AM, Tim Triche, Jr. wrote:
> Yeah, I realized that on Friday and forgot to post it. One question, though -- some of the transcripts aren't annotated to a gene (I would also be happy with putative or confirmed ncRNAs, miRNAs, etc, even more so if I could keep them separate -- is there something like a "knownNcRna" track or table outside of UCSC that I should look into for this purpose?).
>
> Should I just throw out all the transcripts without an EntrezGene ID for the time being, then circle back and revisit this when I find the appropriate resource for non-coding but annotated transcripts?
>
> It seems odd that a table of KnownGene transcripts would lack gene IDs for some of the transcripts.
>
> Thanks again for a very useful package,
>
> --t
>
> On Sep 18, 2011, at 10:33 AM, Michael Lawrence<lawrence.michael at gene.com>  wrote:
>
>>
>>
>> On Fri, Sep 16, 2011 at 8:28 PM, Tim Triche, Jr.<ttriche at usc.edu>  wrote:
>> OK, so I took your advice and used
>>
>> transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene::Hsapiens_UCSC_hg19_knownGene_TxDb)
>>
>> and indeed that is quite handy (got all my TSSes forward and reverse for all my probes in seconds, yay!).  Now the question is, how do I use the associated EntrezGene IDs? e.g. the trusty eg.Hs.org.db says...
>>
>>> elementMetadata(foo)$tx_name[1]
>> [1] "uc001aaa.3"
>>> org.Hs.egSYMBOL[[ elementMetadata(foo)$tx_name[1] ]]
>> NULL
>>
>> Two steps forward, one step back.... eventually I will cram all of this into a genoset, though... :-)
>>
>>
>> You do not need to use the org.* packages for this. Just ask transcripts() for the gene_id column. See ?transcripts.
>>
>> Michael
>>
>> thanks!
>>
>> --t
>>
>>
>>
>> On Thu, Sep 15, 2011 at 3:02 PM, Michael Lawrence<lawrence.michael at gene.com>  wrote:
>> Easiest path is to convert the RangedData to a GRanges:
>>
>> as(TSS.human.GRCh37, "GRanges")
>>
>> I might recommend though to get the TSS's from GenomicFeatures::transcripts.
>>
>> Michael
>>
>> On Thu, Sep 15, 2011 at 2:28 PM, Tim Triche, Jr.<tim.triche at gmail.com>  wrote:
>> I have a GenomicRanges object built from interrogated sites and a RangedData
>> object of human (allegedly canonical) transcription start sites, from Julie
>> Zhu's ChIPpeakAnno package.  I want to walk up and down each chromosome and
>> find the nearest forward and reverse strand TSS and their distance from each
>> site.  This seems like it would work:
>>
>>> nearest(cpgranges, TSS.human.GRCh37)
>>
>> But one of the objects isn't the right type:
>>
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function "nearest", for signature
>> "GRanges", "RangedData"
>>
>> What's the right way to solve this problem?  I know about follow() and
>> precede(), but those won't work either until I solve this :-)
>>
>> thanks!
>>
>>
>>
>> --
>> If people do not believe that mathematics is simple, it is only because they
>> do not realize how complicated life is.
>> John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>>
>>
>> --
>> When you emerge in a few years, you can ask someone what you missed, and you'll find it can be summed up in a few minutes.
>>
>> Derek Sivers
>>
>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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