On Fri, Sep 16, 2011 at 8:28 PM, Tim Triche, Jr. <ttriche@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@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@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
>>> >
>>>
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>>>
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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 <http://sivers.org/berklee>
>
>

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