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

[Jinyan Huang]

It seems I need method range.in.probesets and range.in.probes.

On Tue, Dec 14, 2010 at 10:31 AM, Jinyan Huang <jhuang.ceph at gmail.com> wrote:
> 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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>