definition for intergenic SNPs in locateVariants function
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@adaikalavan-ramasamy-5765
Last seen 10.1 years ago
United Kingdom
Dear all, I have been using the locateVariants function in the VariantAnnotation package. It has been great and we are now in the process of writing the methods section. May I know how the intergenic SNPs were defined? What is the limit upstream and downstream to define PRECEDEID and FOLLOWID. I check the manuals and mailing list without much luck. This is of less importance but is there a way to adjust these definition/limit if we want to do so in future? Thank you. Regards, Adai [[alternative HTML version deleted]]
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@valerie-obenchain-4275
Last seen 2.9 years ago
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Hi Adai, The intergenic SNPs are those that fall outside of the gene ranges defined in the annotation. There is a table in the vignette that briefly describes this. With a txdb as the annotation, "transcripts by gene" are extracted and findOverlaps() is performed with the variant ranges. Variants that do not have a 'hit' are considered to fall outside gene regions. For these variants we determine which genes fall to either side (PREDEDEID and FOLLOWID in the output). There is no limit for upstream/downstream searching. We simply take the next closest gene if one exists. If you were able to define upsteam/downstream limits I'm assuming you're interested in all genes that fell in that range, not just the next closest gene? Valerie On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > Dear all, > > I have been using the locateVariants function in the VariantAnnotation > package. It has been great and we are now in the process of writing the > methods section. > > May I know how the intergenic SNPs were defined? What is the limit upstream > and downstream to define PRECEDEID and FOLLOWID. I check the manuals and > mailing list without much luck. > > This is of less importance but is there a way to adjust these > definition/limit if we want to do so in future? Thank you. > > Regards, Adai > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Dear Valerie, Do you mean there is no limit on the flanking gene? Even if it is say 10Mb away? I am working on eQTLs where most people assume the cis-eQTLs operate on a gene located a short distance away (< 1Mb) so we may want to treat those that are located very far away differently. Thanks. Regards, Adai On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > Hi Adai, > > The intergenic SNPs are those that fall outside of the gene ranges defined > in the annotation. There is a table in the vignette that briefly describes > this. > > With a txdb as the annotation, "transcripts by gene" are extracted and > findOverlaps() is performed with the variant ranges. Variants that do not > have a 'hit' are considered to fall outside gene regions. For these > variants we determine which genes fall to either side (PREDEDEID and > FOLLOWID in the output). There is no limit for upstream/downstream > searching. We simply take the next closest gene if one exists. > > If you were able to define upsteam/downstream limits I'm assuming you're > interested in all genes that fell in that range, not just the next closest > gene? > > Valerie > > > > > On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > >> Dear all, >> >> I have been using the locateVariants function in the VariantAnnotation >> package. It has been great and we are now in the process of writing the >> methods section. >> >> May I know how the intergenic SNPs were defined? What is the limit >> upstream >> and downstream to define PRECEDEID and FOLLOWID. I check the manuals and >> mailing list without much luck. >> >> This is of less importance but is there a way to adjust these >> definition/limit if we want to do so in future? Thank you. >> >> Regards, Adai >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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On 04/03/13 17:10, Adaikalavan Ramasamy wrote: > Dear Valerie, > > Do you mean there is no limit on the flanking gene? Even if it is say > 10Mb away? Yes, that's correct. Since upstream/downstream distance is relevant for eQTL analysis it sounds like this functionality would be useful for a wider audience. I've put this on my TODO for the next devel cycle. Thanks for the suggestion. Valerie > > I am working on eQTLs where most people assume the cis-eQTLs operate on > a gene located a short distance away (< 1Mb) so we may want to treat > those that are located very far away differently. Thanks. > > Regards, Adai > > > > > On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain <vobencha at="" fhcrc.org=""> <mailto:vobencha at="" fhcrc.org="">> wrote: > > Hi Adai, > > The intergenic SNPs are those that fall outside of the gene ranges > defined in the annotation. There is a table in the vignette that > briefly describes this. > > With a txdb as the annotation, "transcripts by gene" are extracted > and findOverlaps() is performed with the variant ranges. Variants > that do not have a 'hit' are considered to fall outside gene > regions. For these variants we determine which genes fall to either > side (PREDEDEID and FOLLOWID in the output). There is no limit for > upstream/downstream searching. We simply take the next closest gene > if one exists. > > If you were able to define upsteam/downstream limits I'm assuming > you're interested in all genes that fell in that range, not just the > next closest gene? > > Valerie > > > > > On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > > Dear all, > > I have been using the locateVariants function in the > VariantAnnotation > package. It has been great and we are now in the process of > writing the > methods section. > > May I know how the intergenic SNPs were defined? What is the > limit upstream > and downstream to define PRECEDEID and FOLLOWID. I check the > manuals and > mailing list without much luck. > > This is of less importance but is there a way to adjust these > definition/limit if we want to do so in future? Thank you. > > Regards, Adai > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >
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@adaikalavan-ramasamy-5765
Last seen 10.1 years ago
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Thanks. That will be a useful feature. In the meantime I will try to delete manually when intergenic snps are too far from the precede or follow ids. Thanks.Valerie Obenchain <vobencha@fhcrc.org> wrote:On 04/03/13 17:10, Adaikalavan Ramasamy wrote: > Dear Valerie, > > Do you mean there is no limit on the flanking gene? Even if it is say > 10Mb away? Yes, that's correct. Since upstream/downstream distance is relevant for eQTL analysis it sounds like this functionality would be useful for a wider audience. I've put this on my TODO for the next devel cycle. Thanks for the suggestion. Valerie > > I am working on eQTLs where most people assume the cis-eQTLs operate on > a gene located a short distance away (< 1Mb) so we may want to treat > those that are located very far away differently. Thanks. > > Regards, Adai > > > > > On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain <vobencha@fhcrc.org> <mailto:vobencha@fhcrc.org>> wrote: > >     Hi Adai, > >     The intergenic SNPs are those that fall outside of the gene ranges >     defined in the annotation. There is a table in the vignette that >     briefly describes this. > >     With a txdb as the annotation, "transcripts by gene" are extracted >     and findOverlaps() is performed with the variant ranges. Variants >     that do not have a 'hit' are considered to fall outside gene >     regions. For these variants we determine which genes fall to either >     side (PREDEDEID and FOLLOWID in the output). There is no limit for >     upstream/downstream searching. We simply take the next closest gene >     if one exists. > >     If you were able to define upsteam/downstream limits I'm assuming >     you're interested in all genes that fell in that range, not just the >     next closest gene? > >     Valerie > > > > >     On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > >         Dear all, > >         I have been using the locateVariants function in the >         VariantAnnotation >         package. It has been great and we are now in the process of >         writing the >         methods section. > >         May I know how the intergenic SNPs were defined? What is the >         limit upstream >         and downstream to define PRECEDEID and FOLLOWID. I check the >         manuals and >         mailing list without much luck. > >         This is of less importance but is there a way to adjust these >         definition/limit if we want to do so in future? Thank you. > >         Regards, Adai > >                  [[alternative HTML version deleted]] > >         _________________________________________________ >         Bioconductor mailing list >         Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >         https://stat.ethz.ch/mailman/__listinfo/bioconductor >         <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >         Search the archives: >        http://news.gmane.org/gmane.__science.biology.informatics.__conductor >        <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > >     _________________________________________________ >     Bioconductor mailing list >     Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >     https://stat.ethz.ch/mailman/__listinfo/bioconductor >     <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >     Search the archives: >    http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > [[alternative HTML version deleted]]
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Thanks Valerie. One more question if you don't mind. I am annotating several thousand SNPs. The number of SNPs allocated to 3'UTR or 5'UTR are exactly the same. I will have expected more from the 3'UTR as the 3'UTR is much longer than 5'UTR. Is this a lucky coincidence? Sorry for the vagueness of the question. Thanks. On Thu, Apr 4, 2013 at 11:56 AM, Adaikalavan Ramasamy < adaikalavan.ramasamy@gmail.com> wrote: > Thanks. That will be a useful feature. > > In the meantime I will try to delete manually when intergenic snps are too > far from the precede or follow ids. Thanks. > > Thanks. That will be a useful feature. > > In the meantime I will try to delete manually when intergenic snps are too > far from the precede or follow ids. Thanks. > Valerie Obenchain <vobencha@fhcrc.org> wrote: > On 04/03/13 17:10, Adaikalavan Ramasamy wrote: > > Dear Valerie, > > > > Do you mean there is no limit on the flanking gene? Even if it is say > > 10Mb away? > > Yes, that's correct. > > Since upstream/downstream distance is relevant for eQTL analysis it > sounds like this functionality would be useful for a wider audience. > I've put this on my TODO for the next devel cycle. Thanks for the > suggestion. > > Valerie > > > > I am working on eQTLs where most people assume the cis-eQTLs operate on > > a gene located a short distance away (< 1Mb) so we may want to treat > > those that are located very far away differently. Thanks. > > > > Regards, Adai > > > > > > > > > > On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain <vobencha@fhcrc.org> > <mailto:vobencha@fhcrc.org>> wrote: > > > > Hi Adai, > > > > The intergenic SNPs are those that fall outside of the gene ranges > > defined in the annotation. There is a table in the vignette that > > briefly describes this. > > > > With a txdb as the annotation, "transcripts by gene" are extracted > > and findOverlaps() is performed with the variant ranges. Variants > > that do not have a 'hit' are considered to fall outside gene > > regions. For these variants we determine which genes fall to either > > side (PREDEDEID and FOLLOWID in the output). There is no limit for > > upstream/downstream searching. We simply take the next closest gene > > if one exists. > > > > If you were able to define upsteam/downstream limits I'm assuming > > you're interested in all genes that fell in that range, not just the > > next closest gene? > > > > Valerie > > > > > > > > > > On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > > > > Dear all, > > > > I have been using the locateVariants function in the > > VariantAnnotation > > package. It has been great and we are now in the process of > > writing the > > methods section. > > > > May I know how the intergenic SNPs were defined? What is the > > limit upstream > > and downstream to define PRECEDEID and FOLLOWID. I check the > > manuals and > > mailing list without much luck. > > > > This is of less importance but is there a way to adjust these > > definition/limit if we want to do so in future? Thank you. > > > > Regards, Adai > > > > [[alternative HTML version deleted]] > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > > < > http://news.gmane.org/gmane.science.biology.informatics.conductor> > > > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor < > http://news.gmane.org/gmane.science.biology.informatics.conductor> > > > > > > > On 04/03/13 17:10, Adaikalavan Ramasamy wrote: > > Dear Valerie, > > > > Do you mean there is no limit on the flanking gene? Even if it is say > > 10Mb away? > > Yes, that's correct. > > Since upstream/downstream distance is relevant for eQTL analysis it > sounds like this functionality would be useful for a wider audience. > I've put this on my TODO for the next devel cycle. Thanks for the > suggestion. > > Valerie > > > > I am working on eQTLs where most people assume the cis-eQTLs operate on > > a gene located a short distance away (< 1Mb) so we may want to treat > > those that are located very far away differently. Thanks. > > > > Regards, Adai > > > > > > > > > > On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain <vobencha@fhcrc.org> > <mailto:vobencha@fhcrc.org>> wrote: > > > > Hi Adai, > > > > The intergenic SNPs are those that fall outside of the gene ranges > > defined in the annotation. There is a table in the vignette that > > briefly describes this. > > > > With a txdb as the annotation, "transcripts by gene" are extracted > > and findOverlaps() is performed with the variant ranges. Variants > > that do not have a 'hit' are considered to fall outside gene > > regions. For these variants we determine which genes fall to either > > side (PREDEDEID and FOLLOWID in the output). There is no limit for > > upstream/downstream searching. We simply take the next closest gene > > if one exists. > > > > If you were able to define upsteam/downstream limits I'm assuming > > you're interested in all genes that fell in that range, not just the > > next closest gene? > > > > Valerie > > > > > > > > > > On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > > > > Dear all, > > > > I have been using the locateVariants function in the > > VariantAnnotation > > package. It has been great and we are now in the process of > > writing the > > methods section. > > > > May I know how the intergenic SNPs were defined? What is the > > limit upstream > > and downstream to define PRECEDEID and FOLLOWID. I check the > > manuals and > > mailing list without much luck. > > > > This is of less importance but is there a way to adjust these > > definition/limit if we want to do so in future? Thank you. > > > > Regards, Adai > > > > [[alternative HTML version deleted]] > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > > < > http://news.gmane.org/gmane.science.biology.informatics.conductor> > > > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor < > http://news.gmane.org/gmane.science.biology.informatics.conductor> > > > > > > > [[alternative HTML version deleted]]
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Hello, I've added 'upstream' and 'downstream' arguments to IntergenicVariants() in VariantAnnotation 1.7.1. You can get it from svn now or use biocLite("VariantAnnotaion") tomorrow after 9am PST. The default values for both are 1e+06 but I am open to changing this if other values make more sense. > IntergenicVariants() class: IntergenicVariants upstream: 1000000 downstream: 1000000 Note that AllVariants() now has 'upstream' and 'downstream' for both PromoterVariants() and IntergenicVariants(). > AllVariants() class: AllVariants promoter: upstream: 2000 downstream: 200 intergenic: upstream: 1000000 downstream: 1000000 Modifying values: IntergenicVariants(500, 500) AllVariants(intergenic=IntergenicVariants(500, 500)) Extracting values: av <- AllVariants(intergenic=IntergenicVariants(500, 500)) intergenic(av) Regarding the utr question, yes, I think it's odd that you would have the same number for 3' and 5'. You can investigate further by extracting the utr regions from your annotation and overlapping those with your variants. Using hg19.knownGene as an example, library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene utr3 <- threeUTRsByTranscript(txdb) utr5 <- fiveUTRsByTranscript(txdb) Use findOverlaps() with these regions and the variants in question to confirm results. Valerie On 04/05/2013 05:39 AM, Adaikalavan Ramasamy wrote: > Thanks Valerie. > > One more question if you don't mind. I am annotating several thousand > SNPs. The number of SNPs allocated to 3'UTR or 5'UTR are exactly the > same. I will have expected more from the 3'UTR as the 3'UTR is much > longer than 5'UTR. Is this a lucky coincidence? Sorry for the vagueness > of the question. Thanks. > > > > On Thu, Apr 4, 2013 at 11:56 AM, Adaikalavan Ramasamy > <adaikalavan.ramasamy at="" gmail.com="" <mailto:adaikalavan.ramasamy="" at="" gmail.com="">> > wrote: > > Thanks. That will be a useful feature. > > In the meantime I will try to delete manually when intergenic snps > are too far from the precede or follow ids. Thanks. > > Thanks. That will be a useful feature. > > In the meantime I will try to delete manually when intergenic snps > are too far from the precede or follow ids. Thanks. > Valerie Obenchain <vobencha at="" fhcrc.org="" <mailto:vobencha="" at="" fhcrc.org="">> > wrote: > On 04/03/13 17:10, Adaikalavan Ramasamy wrote: > > Dear Valerie, > > > > Do you mean there is no limit on the flanking gene? Even if it is say > > 10Mb away? > > Yes, that's correct. > > Since upstream/downstream distance is relevant for eQTL analysis it > sounds like this functionality would be useful for a wider audience. > I've put this on my TODO for the next devel cycle. Thanks for the > suggestion. > > Valerie > > > > I am working on eQTLs where most people assume the cis-eQTLs > operate on > > a gene located a short distance away (< 1Mb) so we may want to treat > > those that are located very far away differently. Thanks. > > > > Regards, Adai > > > > > > > > > > On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain > <vobencha at="" fhcrc.org="" <mailto:vobencha="" at="" fhcrc.org=""> > > <mailto:vobencha at="" fhcrc.org="" <mailto:vobencha="" at="" fhcrc.org="">>> wrote: > > > > Hi Adai, > > > > The intergenic SNPs are those that fall outside of the gene > ranges > > defined in the annotation. There is a table in the vignette that > > briefly describes this. > > > > With a txdb as the annotation, "transcripts by gene" are > extracted > > and findOverlaps() is performed with the variant ranges. Variants > > that do not have a 'hit' are considered to fall outside gene > > regions. For these variants we determine which genes fall to > either > > side (PREDEDEID and FOLLOWID in the output). There is no > limit for > > upstream/downstream searching. We simply take the next > closest gene > > if one exists. > > > > If you were able to define upsteam/downstream limits I'm assuming > > you're interested in all genes that fell in that range, not > just the > > next closest gene? > > > > Valerie > > > > > > > > > > On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > > > > Dear all, > > > > I have been using the locateVariants function in the > > VariantAnnotation > > package. It has been great and we are now in the process of > > writing the > > methods section. > > > > May I know how the intergenic SNPs were defined? What is the > > limit upstream > > and downstream to define PRECEDEID and FOLLOWID. I check the > > manuals and > > mailing list without much luck. > > > > This is of less importance but is there a way to adjust these > > definition/limit if we want to do so in future? Thank you. > > > > Regards, Adai > > > > [[alternative HTML version deleted]] > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org="" <mailto:bioconductor="" at="" r-project.org="">> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > > > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org="" <mailto:bioconductor="" at="" r-project.org="">> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > > > On 04/03/13 17:10, Adaikalavan Ramasamy wrote: > > Dear Valerie, > > > > Do you mean there is no limit on the flanking gene? Even if it is say > > 10Mb away? > > Yes, that's correct. > > Since upstream/downstream distance is relevant for eQTL analysis it > sounds like this functionality would be useful for a wider audience. > I've put this on my TODO for the next devel cycle. Thanks for the > suggestion. > > Valerie > > > > I am working on eQTLs where most people assume the cis-eQTLs > operate on > > a gene located a short distance away (< 1Mb) so we may want to treat > > those that are located very far away differently. Thanks. > > > > Regards, Adai > > > > > > > > > > On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain > <vobencha at="" fhcrc.org="" <mailto:vobencha="" at="" fhcrc.org=""> > > <mailto:vobencha at="" fhcrc.org="" <mailto:vobencha="" at="" fhcrc.org="">>> wrote: > > > > Hi Adai, > > > > The intergenic SNPs are those that fall outside of the gene > ranges > > defined in the annotation. There is a table in the vignette that > > briefly describes this. > > > > With a txdb as the annotation, "transcripts by gene" are > extracted > > and findOverlaps() is performed with the variant ranges. Variants > > that do not have a 'hit' are considered to fall outside gene > > regions. For these variants we determine which genes fall to > either > > side (PREDEDEID and FOLLOWID in the output). There is no > limit for > > upstream/downstream searching. We simply take the next > closest gene > > if one exists. > > > > If you were able to define upsteam/downstream limits I'm assuming > > you're interested in all genes that fell in that range, not > just the > > next closest gene? > > > > Valerie > > > > > > > > > > On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote: > > > > Dear all, > > > > I have been using the locateVariants function in the > > VariantAnnotation > > package. It has been great and we are now in the process of > > writing the > > methods section. > > > > May I know how the intergenic SNPs were defined? What is the > > limit upstream > > and downstream to define PRECEDEID and FOLLOWID. I check the > > manuals and > > mailing list without much luck. > > > > This is of less importance but is there a way to adjust these > > definition/limit if we want to do so in future? Thank you. > > > > Regards, Adai > > > > [[alternative HTML version deleted]] > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org="" <mailto:bioconductor="" at="" r-project.org="">> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > > > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > > _________________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org="" <mailto:bioconductor="" at="" r-project.org="">> > > https://stat.ethz.ch/mailman/__listinfo/bioconductor > > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > > Search the archives: > > > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > > >
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