Xmapcore package: check a position whether it is in a probe or probeset.
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Tim Yates ▴ 250
@tim-yates-4040
Last seen 8.4 years ago
Can't you use probeset.in.range or probe.in.range? Tim -----Original Message----- From: hiekeen@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. -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}
probe xmapcore probe xmapcore • 813 views
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Tim Yates ▴ 250
@tim-yates-4040
Last seen 8.4 years ago
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@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. -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}
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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. > -------------------------------------------------------- > This email is confidential and intended solely for the...{{dropped:13}}
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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. >> -------------------------------------------------------- >> This email is confidential and intended solely for the use of the person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Paterson Institute for Cancer Research or the University of Manchester. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible. >> >
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