[BioC] microRNA hg build?

[James F. Reid]

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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