[BioC] microRNA hg build?

[James F. Reid]

sorry, the last statement should be just 'print(tsCoords)', remove the n=3.

J.

On 05/18/2011 02:01 PM, James F. Reid wrote:
> Hi Tim / Jinyan,
>
> now I understand what you are trying to do.
> You probably want to use the rtracklayer library to access the hg19
> targetscan tables provided by ucsc:
>
> library("rtracklayer")
> session <- browserSession()
> genome(session) <- "hg19"
> query <- ucscTableQuery(session, "TS miRNA sites", genome(session))
> print(query)
> tableNames(query)
> tsCoords <- track(query)
> print(tsCoords, n=3)
>
> HTH,
> J.
>
>
> On 05/17/2011 10:48 PM, Jinyan Huang wrote:
>> Marc,
>>
>> Thank you for your information. I prefer hg19. In my analysis, I have
>> a list snp. I want to check whether this snp is in the microRNA in the
>> binding sites or not. I do not know whick packages is better.
>>
>> Thanks.
>>
>> On Tue, May 17, 2011 at 10:41 PM, Marc Carlson<mcarlson at fhcrc.org> wrote:
>>> Marc
>>
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