[BioC] Xmapcore package: check a position whether it is in a probe or probeset.

[Jinyan Huang]

Tim,
Thanks for your reply.
I have try probesets.in.range. It is not working for my purpose. Given
a snp, I want to check whether this snp is within a probeset or not.
For example, for probeset, 3067144, the location is
chr7:107002769-107002822 (-)

I use probesets.in.range to check chr7:107002799. I do like this:

> library("xmapcore")
> xmap.connect("hs")
Using /env/ceph/home/jhuang//.xmapcore as our configuration directory
Connected to xmapcore_homo_sapiens_58 (localhost)
Selected array 'HuEx-1_0' as a default.
> probesets.in.range("7",107002799,107002799,-1)
NULL
> probesets.in.range("7",107002799,107002800,-1)
NULL
> probesets.in.range("7",107002799,107002822,-1)
NULL
> probesets.in.range("7",107002769,107002822,-1)
[1] "3067144"

BTW: is it possible to search in two strand in the same time?

So it seems probesets.in.range need a range, not a fixed position. Do
you have any others suggestions?

Thank you very much in advance.




On Tue, Dec 14, 2010 at 1:36 AM, Tim Yates <TYates at picr.man.ac.uk> wrote:
>
> Sorry, I meant the plural:
>
>  probesets.in.range
>
> or
>
>  probes.in.range
>
> Tim
>
> -----Original Message-----
> From: Tim Yates
> Sent: Tue 12/14/2010 12:35 AM
> To: Jinyan Huang; Bioconductor mailing list
> Subject: RE: Xmapcore package: check a position whether it is in a probe or probeset.
>
>
> Can't you use probeset.in.range or probe.in.range?
>
> Tim
>
> -----Original Message-----
> From: hiekeen at gmail.com on behalf of Jinyan Huang
> Sent: Mon 12/13/2010 11:29 PM
> To: Bioconductor mailing list; Tim Yates
> Subject: Xmapcore package: check a position whether it is in a probe or probeset.
>
> Dear all,
>
> Given a genome position (SNP), I want to know this position (SNP) is
> in a  probe or probeset or not. Can Xmapcore have this function? The
> probe and probeset is for HuEx-1_0 array.
>
> Thanks.
> --------------------------------------------------------
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