Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?
1
0
Entering edit mode
Adriana Munoz ▴ 100
@adriana-munoz-4936
Last seen 7.1 years ago
> > > Hello, > > I'd like to ask you if there is an attribute to extract SNP function information from variation datasets in biomaRt such as synonymous, nonsynonymous, etc and > > a related filter. > > I'm using the following rcode: snpmart = useMart("snp", dataset="hsapiens_snp") > Any help will be appreciated. > > Thanks, > > Adriana > > [[alternative HTML version deleted]]
SNP biomaRt SNP biomaRt • 1.2k views
ADD COMMENT
0
Entering edit mode
@valerie-obenchain-4275
Last seen 23 months ago
United States
Hi Adriana, I believe the filter you want is consequence_type. Take a look at the filters available to you with, listFilters(snpmart) You may also want to take a look at the VariantAnnotation package. There are functions ?locateVariants ?predictCoding that can tell you where your variant is located (coding, non-coding, utr, etc.) and provide the amino acid coding change is for the non-synonymous variants. Recently SIFT and PolyPhen scores have been made available through db packages SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. Valerie On 11/02/2011 07:33 AM, Adriana Munoz wrote: >> >> Hello, >> >> I'd like to ask you if there is an attribute to extract SNP function information from variation datasets in biomaRt such as synonymous, nonsynonymous, etc and >> >> a related filter. >> >> I'm using the following rcode: > snpmart = useMart("snp", dataset="hsapiens_snp") > >> Any help will be appreciated. >> >> Thanks, >> >> Adriana >> >> > [[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
ADD COMMENT
0
Entering edit mode
Hi Valerie, Thanks for the information. I used the filter you mentioned and it works. I'd like to try the Variant Annotation package that you mentioned to get where my variant is located (coding, non-coding, utr, etc.) , too, but I got the following error message in my Mac: "Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘VariantAnnotation’ is not available (for R version 2.13.2)" Then, I tried loading the package in Windows that has R version 2.12., but I the following error message: "Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘VariantAnnotation’ is not available" May I ask you if you know by chance what version of R you were running for the Variant Annotation package? or do you know of any attributes and filters in Biomart to get where my variant is located (coding, non- coding, utr, etc.)? Thanks, Adriana On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > Hi Adriana, > > I believe the filter you want is consequence_type. Take a look at the > filters available to you with, > > listFilters(snpmart) > > You may also want to take a look at the VariantAnnotation package. There > are functions > > ?locateVariants > ?predictCoding > > that can tell you where your variant is located (coding, non-coding, utr, > etc.) and provide the amino acid coding change is for the non- synonymous > variants. Recently SIFT and PolyPhen scores have been made available > through db packages > SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. > > Valerie > > > > > > > On 11/02/2011 07:33 AM, Adriana Munoz wrote: > >> >>> Hello, >>> >>> I'd like to ask you if there is an attribute to extract SNP function >>> information from variation datasets in biomaRt such as synonymous, >>> nonsynonymous, etc and >>> >>> a related filter. >>> >>> I'm using the following rcode: >>> >> snpmart = useMart("snp", dataset="hsapiens_snp") >> >> Any help will be appreciated. >>> >>> Thanks, >>> >>> Adriana >>> >>> >>> [[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=""> >> > > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
As far as I remember, only available since R 2.14. Cheers Xavier On 11/11/11 18:16, Adriana Munoz wrote: > Hi Valerie, > > Thanks for the information. I used the filter you mentioned and it works. > I'd like to try the Variant Annotation package that you mentioned to > get where my variant is located (coding, non-coding, utr, etc.) , too, but > I got the following error message in my Mac: > "Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?VariantAnnotation? is not available (for R version 2.13.2)" > > Then, I tried loading the package in Windows that has R version 2.12., but > I the following error message: > "Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?VariantAnnotation? is not available" > > May I ask you if you know by chance what version of R you were running for > the Variant Annotation package? or do you know of any attributes and > filters in Biomart to get where my variant is located (coding, non- coding, > utr, etc.)? > > Thanks, > > Adriana > > On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain<vobencha at="" fhcrc.org="">wrote: > >> Hi Adriana, >> >> I believe the filter you want is consequence_type. Take a look at the >> filters available to you with, >> >> listFilters(snpmart) >> >> You may also want to take a look at the VariantAnnotation package. There >> are functions >> >> ?locateVariants >> ?predictCoding >> >> that can tell you where your variant is located (coding, non- coding, utr, >> etc.) and provide the amino acid coding change is for the non- synonymous >> variants. Recently SIFT and PolyPhen scores have been made available >> through db packages >> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. >> >> Valerie >> >> >> >> >> >> >> On 11/02/2011 07:33 AM, Adriana Munoz wrote: >> >>>> Hello, >>>> >>>> I'd like to ask you if there is an attribute to extract SNP function >>>> information from variation datasets in biomaRt such as synonymous, >>>> nonsynonymous, etc and >>>> >>>> a related filter. >>>> >>>> I'm using the following rcode: >>>> >>> snpmart = useMart("snp", dataset="hsapiens_snp") >>> >>> Any help will be appreciated. >>>> Thanks, >>>> >>>> Adriana >>>> >>>> >>>> [[alternative HTML version deleted]] >>>>
ADD REPLY
0
Entering edit mode
On 11/14/2011 12:16 AM, Xavier de Pedro wrote: > As far as I remember, only available since R 2.14. > Cheers > Xavier > Yes, that is correct. You'll need R-2.14 for VariantAnnotation. To find the locations of your variant with biomaRt you could try 'consequence_type_tv' as the attribute then filter on the value you want with 'consequence_type'. ## Here we select a group of snps from chr8: snps_all<- getBM(c('refsnp_id','allele','chrom_start','chrom_strand', 'consequence_type_tv', 'set_description', 'set_name'), filters = c('chr_name','chrom_start','chrom_end'), values = list(8,148350,158612), mart = snpmart) ## List the possible values for 'consequence_type_tv': > unique(snps_all$consequence_type_tv) [1] "INTRONIC" [2] "DOWNSTREAM" [3] "SYNONYMOUS_CODING" [4] "WITHIN_NON_CODING_GENE" [5] "NON_SYNONYMOUS_CODING" [6] "UPSTREAM" [7] "WITHIN_NON_CODING_GENE&INTRONIC&SPLICE_SITE" [8] "WITHIN_NON_CODING_GENE&INTRONIC" [9] "WITHIN_NON_CODING_GENE&SPLICE_SITE" [10] "" ## Select only nonsynonymous coding snps: snps_nsc <- getBM(c('refsnp_id','allele','chrom_start','chrom_strand', 'consequence_type_tv', 'set_description', 'set_name'), filters = c('chr_name','chrom_start','chrom_end', 'consequence_type'), values = list(8,148350,158612, 'NON_SYNONYMOUS_CODING'), mart = snpmart) Valerie > On 11/11/11 18:16, Adriana Munoz wrote: >> Hi Valerie, >> >> Thanks for the information. I used the filter you mentioned and it >> works. >> I'd like to try the Variant Annotation package that you mentioned to >> get where my variant is located (coding, non-coding, utr, etc.) , >> too, but >> I got the following error message in my Mac: >> "Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ?VariantAnnotation? is not available (for R version 2.13.2)" >> >> Then, I tried loading the package in Windows that has R version >> 2.12., but >> I the following error message: >> "Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ?VariantAnnotation? is not available" >> >> May I ask you if you know by chance what version of R you were >> running for >> the Variant Annotation package? or do you know of any attributes and >> filters in Biomart to get where my variant is located (coding, >> non-coding, >> utr, etc.)? >> >> Thanks, >> >> Adriana >> >> On Tue, Nov 8, 2011 at 7:37 PM, Valerie >> Obenchain<vobencha at="" fhcrc.org="">wrote: >> >>> Hi Adriana, >>> >>> I believe the filter you want is consequence_type. Take a look at the >>> filters available to you with, >>> >>> listFilters(snpmart) >>> >>> You may also want to take a look at the VariantAnnotation package. >>> There >>> are functions >>> >>> ?locateVariants >>> ?predictCoding >>> >>> that can tell you where your variant is located (coding, non- coding, >>> utr, >>> etc.) and provide the amino acid coding change is for the >>> non-synonymous >>> variants. Recently SIFT and PolyPhen scores have been made available >>> through db packages >>> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. >>> >>> Valerie >>> >>> >>> >>> >>> >>> >>> On 11/02/2011 07:33 AM, Adriana Munoz wrote: >>> >>>>> Hello, >>>>> >>>>> I'd like to ask you if there is an attribute to extract SNP function >>>>> information from variation datasets in biomaRt such as synonymous, >>>>> nonsynonymous, etc and >>>>> >>>>> a related filter. >>>>> >>>>> I'm using the following rcode: >>>>> >>>> snpmart = useMart("snp", dataset="hsapiens_snp") >>>> >>>> Any help will be appreciated. >>>>> Thanks, >>>>> >>>>> Adriana >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >
ADD REPLY
0
Entering edit mode
Thanks so much for the information on the use of that filter. I could extract the synonymous SNPs that I needed. Do you know if there is any difference between using single quotes (') and double quotes (") for the labels? Would it be safe to assume that the SNPs that are extracted using the filter value 'NON_SYNONYMOUS_CODING' would be all different from the SNPs that are extracted using the filter value 'SYNONYMOUS_CODING' ? When I listed the possible values for 'consequence_type_tv', I got one of them labeled "SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING" Do you know by chance the meaning of this type of SNP? or do you know where to find documentation about it? I'm trying to extract SNPs that are not "UPSTREAM", so do you know how to write negation condition in the getBM command or more complex expressions with negation, patterns (etc)? Thanks, Adriana On Mon, Nov 14, 2011 at 12:44 PM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > On 11/14/2011 12:16 AM, Xavier de Pedro wrote: > >> As far as I remember, only available since R 2.14. >> Cheers >> Xavier >> >> > Yes, that is correct. You'll need R-2.14 for VariantAnnotation. > > To find the locations of your variant with biomaRt you could try > 'consequence_type_tv' as the attribute then filter on the value you want > with 'consequence_type'. > > ## Here we select a group of snps from chr8: > snps_all<- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', > 'consequence_type_tv', 'set_description', 'set_name'), > filters = c('chr_name','chrom_start','** > chrom_end'), > values = list(8,148350,158612), > mart = snpmart) > > ## List the possible values for 'consequence_type_tv': > > unique(snps_all$consequence_**type_tv) > [1] "INTRONIC" > [2] "DOWNSTREAM" > [3] "SYNONYMOUS_CODING" > [4] "WITHIN_NON_CODING_GENE" > [5] "NON_SYNONYMOUS_CODING" > [6] "UPSTREAM" > [7] "WITHIN_NON_CODING_GENE&**INTRONIC&SPLICE_SITE" > [8] "WITHIN_NON_CODING_GENE&**INTRONIC" > [9] "WITHIN_NON_CODING_GENE&**SPLICE_SITE" > [10] "" > > ## Select only nonsynonymous coding snps: > snps_nsc <- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', > 'consequence_type_tv', 'set_description', 'set_name'), > filters = c('chr_name','chrom_start','**chrom_end', > 'consequence_type'), > values = list(8,148350,158612, > 'NON_SYNONYMOUS_CODING'), > mart = snpmart) > > Valerie > > On 11/11/11 18:16, Adriana Munoz wrote: >> >>> Hi Valerie, >>> >>> Thanks for the information. I used the filter you mentioned and it >>> works. >>> I'd like to try the Variant Annotation package that you mentioned to >>> get where my variant is located (coding, non-coding, utr, etc.) , too, >>> but >>> I got the following error message in my Mac: >>> "Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package ‘VariantAnnotation’ is not available (for R version 2.13.2)" >>> >>> Then, I tried loading the package in Windows that has R version 2.12., >>> but >>> I the following error message: >>> "Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package ‘VariantAnnotation’ is not available" >>> >>> May I ask you if you know by chance what version of R you were running >>> for >>> the Variant Annotation package? or do you know of any attributes and >>> filters in Biomart to get where my variant is located (coding, >>> non-coding, >>> utr, etc.)? >>> >>> Thanks, >>> >>> Adriana >>> >>> On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain<vobencha@fhcrc.org>** >>> wrote: >>> >>> Hi Adriana, >>>> >>>> I believe the filter you want is consequence_type. Take a look at the >>>> filters available to you with, >>>> >>>> listFilters(snpmart) >>>> >>>> You may also want to take a look at the VariantAnnotation package. There >>>> are functions >>>> >>>> ?locateVariants >>>> ?predictCoding >>>> >>>> that can tell you where your variant is located (coding, non- coding, >>>> utr, >>>> etc.) and provide the amino acid coding change is for the non- synonymous >>>> variants. Recently SIFT and PolyPhen scores have been made available >>>> through db packages >>>> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. >>>> >>>> Valerie >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 11/02/2011 07:33 AM, Adriana Munoz wrote: >>>> >>>> Hello, >>>>>> >>>>>> I'd like to ask you if there is an attribute to extract SNP function >>>>>> information from variation datasets in biomaRt such as synonymous, >>>>>> nonsynonymous, etc and >>>>>> >>>>>> a related filter. >>>>>> >>>>>> I'm using the following rcode: >>>>>> >>>>>> snpmart = useMart("snp", dataset="hsapiens_snp") >>>>> >>>>> Any help will be appreciated. >>>>> >>>>>> Thanks, >>>>>> >>>>>> Adriana >>>>>> >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> >> > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
Thanks so much for the information you sent. It's very useful. I was trying to run the following code to get SNPs with 'consequence_type' = "SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING" , but I got error messages: d <- getBM(attributes = c('refsnp_id', 'consequence_type_tv'), filters = c('consequence_type'), values = c("SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING"), mart = snpmart, uniqueRows = TRUE) Error in getBM(attributes = c("refsnp_id", "consequence_type_tv"), filters = c("consequence_type"), : Query ERROR: caught BioMart::Exception: non-BioMart die(): not well-formed (invalid token) at line 1, column 357, byte 357 at /usr/lib/perl5/XML/Parser.pm line 187 d <- getBM(attributes = c('refsnp_id', 'consequence_type_tv'), filters = c('consequence_type'), values = list("SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING"), mart = snpmart, uniqueRows = TRUE) Error in getBM(attributes = c("refsnp_id", "consequence_type_tv"), filters = c("consequence_type"), : Query ERROR: caught BioMart::Exception: non-BioMart die(): not well-formed (invalid token) at line 1, column 357, byte 357 at /usr/lib/perl5/XML/Parser.pm line 187 Do you know what syntax I should use for this case? Please let me know, Thanks, Adriana On Mon, Nov 14, 2011 at 12:44 PM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > On 11/14/2011 12:16 AM, Xavier de Pedro wrote: > >> As far as I remember, only available since R 2.14. >> Cheers >> Xavier >> >> > Yes, that is correct. You'll need R-2.14 for VariantAnnotation. > > To find the locations of your variant with biomaRt you could try > 'consequence_type_tv' as the attribute then filter on the value you want > with 'consequence_type'. > > ## Here we select a group of snps from chr8: > snps_all<- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', > 'consequence_type_tv', 'set_description', 'set_name'), > filters = c('chr_name','chrom_start','** > chrom_end'), > values = list(8,148350,158612), > mart = snpmart) > > ## List the possible values for 'consequence_type_tv': > > unique(snps_all$consequence_**type_tv) > [1] "INTRONIC" > [2] "DOWNSTREAM" > [3] "SYNONYMOUS_CODING" > [4] "WITHIN_NON_CODING_GENE" > [5] "NON_SYNONYMOUS_CODING" > [6] "UPSTREAM" > [7] "WITHIN_NON_CODING_GENE&**INTRONIC&SPLICE_SITE" > [8] "WITHIN_NON_CODING_GENE&**INTRONIC" > [9] "WITHIN_NON_CODING_GENE&**SPLICE_SITE" > [10] "" > > ## Select only nonsynonymous coding snps: > snps_nsc <- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', > 'consequence_type_tv', 'set_description', 'set_name'), > filters = c('chr_name','chrom_start','**chrom_end', > 'consequence_type'), > values = list(8,148350,158612, > 'NON_SYNONYMOUS_CODING'), > mart = snpmart) > > Valerie > > On 11/11/11 18:16, Adriana Munoz wrote: >> >>> Hi Valerie, >>> >>> Thanks for the information. I used the filter you mentioned and it >>> works. >>> I'd like to try the Variant Annotation package that you mentioned to >>> get where my variant is located (coding, non-coding, utr, etc.) , too, >>> but >>> I got the following error message in my Mac: >>> "Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package ‘VariantAnnotation’ is not available (for R version 2.13.2)" >>> >>> Then, I tried loading the package in Windows that has R version 2.12., >>> but >>> I the following error message: >>> "Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package ‘VariantAnnotation’ is not available" >>> >>> May I ask you if you know by chance what version of R you were running >>> for >>> the Variant Annotation package? or do you know of any attributes and >>> filters in Biomart to get where my variant is located (coding, >>> non-coding, >>> utr, etc.)? >>> >>> Thanks, >>> >>> Adriana >>> >>> On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain<vobencha@fhcrc.org>** >>> wrote: >>> >>> Hi Adriana, >>>> >>>> I believe the filter you want is consequence_type. Take a look at the >>>> filters available to you with, >>>> >>>> listFilters(snpmart) >>>> >>>> You may also want to take a look at the VariantAnnotation package. There >>>> are functions >>>> >>>> ?locateVariants >>>> ?predictCoding >>>> >>>> that can tell you where your variant is located (coding, non- coding, >>>> utr, >>>> etc.) and provide the amino acid coding change is for the non- synonymous >>>> variants. Recently SIFT and PolyPhen scores have been made available >>>> through db packages >>>> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. >>>> >>>> Valerie >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 11/02/2011 07:33 AM, Adriana Munoz wrote: >>>> >>>> Hello, >>>>>> >>>>>> I'd like to ask you if there is an attribute to extract SNP function >>>>>> information from variation datasets in biomaRt such as synonymous, >>>>>> nonsynonymous, etc and >>>>>> >>>>>> a related filter. >>>>>> >>>>>> I'm using the following rcode: >>>>>> >>>>>> snpmart = useMart("snp", dataset="hsapiens_snp") >>>>> >>>>> Any help will be appreciated. >>>>> >>>>>> Thanks, >>>>>> >>>>>> Adriana >>>>>> >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> >> > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
Hi Adriana, You're query gets translated into XML and XML doesn't like ampersand's (&) by themselves. You'll have to replace & with & and then it should work. That said, why are you putting these two consequences together in one value. If you want SNPs with both these consequence types you should set values=c('SYNONYMOUS_CODING','NON_SYNONYMOUS_CODING') Cheers, Steffen On Wed, Nov 16, 2011 at 8:31 AM, Adriana Munoz <adri.embo@gmail.com> wrote: > Thanks so much for the information you sent. It's very useful. > > I was trying to run the following code to get SNPs with 'consequence_type' > = "SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING" , but I got error messages: > > d <- getBM(attributes = c('refsnp_id', 'consequence_type_tv'), filters = > c('consequence_type'), values = > c("SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING"), mart = snpmart, uniqueRows = > TRUE) > > Error in getBM(attributes = c("refsnp_id", "consequence_type_tv"), filters > = c("consequence_type"), : > Query ERROR: caught BioMart::Exception: non-BioMart die(): > not well-formed (invalid token) at line 1, column 357, byte 357 at > /usr/lib/perl5/XML/Parser.pm line 187 > > d <- getBM(attributes = c('refsnp_id', 'consequence_type_tv'), filters = > c('consequence_type'), values = > list("SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING"), mart = snpmart, uniqueRows > = TRUE) > > Error in getBM(attributes = c("refsnp_id", "consequence_type_tv"), filters > = c("consequence_type"), : > Query ERROR: caught BioMart::Exception: non-BioMart die(): > not well-formed (invalid token) at line 1, column 357, byte 357 at > /usr/lib/perl5/XML/Parser.pm line 187 > > Do you know what syntax I should use for this case? > > Please let me know, > > Thanks, > > Adriana > > On Mon, Nov 14, 2011 at 12:44 PM, Valerie Obenchain <vobencha@fhcrc.org> >wrote: > > > On 11/14/2011 12:16 AM, Xavier de Pedro wrote: > > > >> As far as I remember, only available since R 2.14. > >> Cheers > >> Xavier > >> > >> > > Yes, that is correct. You'll need R-2.14 for VariantAnnotation. > > > > To find the locations of your variant with biomaRt you could try > > 'consequence_type_tv' as the attribute then filter on the value you want > > with 'consequence_type'. > > > > ## Here we select a group of snps from chr8: > > snps_all<- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', > > 'consequence_type_tv', 'set_description', 'set_name'), > > filters = c('chr_name','chrom_start','** > > chrom_end'), > > values = list(8,148350,158612), > > mart = snpmart) > > > > ## List the possible values for 'consequence_type_tv': > > > unique(snps_all$consequence_**type_tv) > > [1] "INTRONIC" > > [2] "DOWNSTREAM" > > [3] "SYNONYMOUS_CODING" > > [4] "WITHIN_NON_CODING_GENE" > > [5] "NON_SYNONYMOUS_CODING" > > [6] "UPSTREAM" > > [7] "WITHIN_NON_CODING_GENE&**INTRONIC&SPLICE_SITE" > > [8] "WITHIN_NON_CODING_GENE&**INTRONIC" > > [9] "WITHIN_NON_CODING_GENE&**SPLICE_SITE" > > [10] "" > > > > ## Select only nonsynonymous coding snps: > > snps_nsc <- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', > > 'consequence_type_tv', 'set_description', 'set_name'), > > filters = > c('chr_name','chrom_start','**chrom_end', > > 'consequence_type'), > > values = list(8,148350,158612, > > 'NON_SYNONYMOUS_CODING'), > > mart = snpmart) > > > > Valerie > > > > On 11/11/11 18:16, Adriana Munoz wrote: > >> > >>> Hi Valerie, > >>> > >>> Thanks for the information. I used the filter you mentioned and it > >>> works. > >>> I'd like to try the Variant Annotation package that you mentioned to > >>> get where my variant is located (coding, non-coding, utr, etc.) , too, > >>> but > >>> I got the following error message in my Mac: > >>> "Warning message: > >>> In getDependencies(pkgs, dependencies, available, lib) : > >>> package ‘VariantAnnotation’ is not available (for R version 2.13.2)" > >>> > >>> Then, I tried loading the package in Windows that has R version 2.12., > >>> but > >>> I the following error message: > >>> "Warning message: > >>> In getDependencies(pkgs, dependencies, available, lib) : > >>> package ‘VariantAnnotation’ is not available" > >>> > >>> May I ask you if you know by chance what version of R you were running > >>> for > >>> the Variant Annotation package? or do you know of any attributes and > >>> filters in Biomart to get where my variant is located (coding, > >>> non-coding, > >>> utr, etc.)? > >>> > >>> Thanks, > >>> > >>> Adriana > >>> > >>> On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain<vobencha@fhcrc.org> >** > >>> wrote: > >>> > >>> Hi Adriana, > >>>> > >>>> I believe the filter you want is consequence_type. Take a look at the > >>>> filters available to you with, > >>>> > >>>> listFilters(snpmart) > >>>> > >>>> You may also want to take a look at the VariantAnnotation package. > There > >>>> are functions > >>>> > >>>> ?locateVariants > >>>> ?predictCoding > >>>> > >>>> that can tell you where your variant is located (coding, non- coding, > >>>> utr, > >>>> etc.) and provide the amino acid coding change is for the > non-synonymous > >>>> variants. Recently SIFT and PolyPhen scores have been made available > >>>> through db packages > >>>> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. > >>>> > >>>> Valerie > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> On 11/02/2011 07:33 AM, Adriana Munoz wrote: > >>>> > >>>> Hello, > >>>>>> > >>>>>> I'd like to ask you if there is an attribute to extract SNP function > >>>>>> information from variation datasets in biomaRt such as synonymous, > >>>>>> nonsynonymous, etc and > >>>>>> > >>>>>> a related filter. > >>>>>> > >>>>>> I'm using the following rcode: > >>>>>> > >>>>>> snpmart = useMart("snp", dataset="hsapiens_snp") > >>>>> > >>>>> Any help will be appreciated. > >>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> Adriana > >>>>>> > >>>>>> > >>>>>> [[alternative HTML version deleted]] > >>>>>> > >>>>>> > >> > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
Hi Steffen, Thanks so much for your help. I tried and it works! This was just to check how many SNPs had both values. I agree, your code using c() works, too. Do you know how to write negation condition or more complex expressions in the in the filter of the getBM command? For example, to extract SNPs that are not "UPSTREAM", I would write: in the filter .. values = c(not('UPSTREAM')), but I don't know if not() exists. Thanks, Adriana On Wed, Nov 16, 2011 at 11:56 AM, Steffen Durinck <durinck.steffen@gene.com>wrote: > Hi Adriana, > > You're query gets translated into XML and XML doesn't like ampersand's (&) > by themselves. > You'll have to replace & with & and then it should work. > That said, why are you putting these two consequences together in one > value. If you want SNPs with both these consequence types you should set > values=c('SYNONYMOUS_CODING','NON_SYNONYMOUS_CODING') > > Cheers, > Steffen > > On Wed, Nov 16, 2011 at 8:31 AM, Adriana Munoz <adri.embo@gmail.com>wrote: > >> Thanks so much for the information you sent. It's very useful. >> >> I was trying to run the following code to get SNPs with 'consequence_type' >> = "SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING" , but I got error messages: >> >> d <- getBM(attributes = c('refsnp_id', 'consequence_type_tv'), filters = >> c('consequence_type'), values = >> c("SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING"), mart = snpmart, uniqueRows = >> TRUE) >> >> Error in getBM(attributes = c("refsnp_id", "consequence_type_tv"), filters >> = c("consequence_type"), : >> Query ERROR: caught BioMart::Exception: non-BioMart die(): >> not well-formed (invalid token) at line 1, column 357, byte 357 at >> /usr/lib/perl5/XML/Parser.pm line 187 >> >> d <- getBM(attributes = c('refsnp_id', 'consequence_type_tv'), filters = >> c('consequence_type'), values = >> list("SYNONYMOUS_CODING&NON_SYNONYMOUS_CODING"), mart = snpmart, >> uniqueRows >> = TRUE) >> >> Error in getBM(attributes = c("refsnp_id", "consequence_type_tv"), filters >> = c("consequence_type"), : >> Query ERROR: caught BioMart::Exception: non-BioMart die(): >> not well-formed (invalid token) at line 1, column 357, byte 357 at >> /usr/lib/perl5/XML/Parser.pm line 187 >> >> Do you know what syntax I should use for this case? >> >> Please let me know, >> >> Thanks, >> >> Adriana >> >> On Mon, Nov 14, 2011 at 12:44 PM, Valerie Obenchain <vobencha@fhcrc.org>> >wrote: >> >> > On 11/14/2011 12:16 AM, Xavier de Pedro wrote: >> > >> >> As far as I remember, only available since R 2.14. >> >> Cheers >> >> Xavier >> >> >> >> >> > Yes, that is correct. You'll need R-2.14 for VariantAnnotation. >> > >> > To find the locations of your variant with biomaRt you could try >> > 'consequence_type_tv' as the attribute then filter on the value you want >> > with 'consequence_type'. >> > >> > ## Here we select a group of snps from chr8: >> > snps_all<- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', >> >> > 'consequence_type_tv', 'set_description', 'set_name'), >> > filters = c('chr_name','chrom_start','** >> >> > chrom_end'), >> > values = list(8,148350,158612), >> > mart = snpmart) >> > >> > ## List the possible values for 'consequence_type_tv': >> > > unique(snps_all$consequence_**type_tv) >> >> > [1] "INTRONIC" >> > [2] "DOWNSTREAM" >> > [3] "SYNONYMOUS_CODING" >> > [4] "WITHIN_NON_CODING_GENE" >> > [5] "NON_SYNONYMOUS_CODING" >> > [6] "UPSTREAM" >> > [7] "WITHIN_NON_CODING_GENE&**INTRONIC&SPLICE_SITE" >> > [8] "WITHIN_NON_CODING_GENE&**INTRONIC" >> > [9] "WITHIN_NON_CODING_GENE&**SPLICE_SITE" >> > [10] "" >> > >> > ## Select only nonsynonymous coding snps: >> > snps_nsc <- getBM(c('refsnp_id','allele','**chrom_start','chrom_strand', >> >> > 'consequence_type_tv', 'set_description', 'set_name'), >> > filters = >> c('chr_name','chrom_start','**chrom_end', >> >> > 'consequence_type'), >> > values = list(8,148350,158612, >> > 'NON_SYNONYMOUS_CODING'), >> > mart = snpmart) >> > >> > Valerie >> > >> > On 11/11/11 18:16, Adriana Munoz wrote: >> >> >> >>> Hi Valerie, >> >>> >> >>> Thanks for the information. I used the filter you mentioned and it >> >>> works. >> >>> I'd like to try the Variant Annotation package that you mentioned to >> >>> get where my variant is located (coding, non-coding, utr, etc.) , too, >> >>> but >> >>> I got the following error message in my Mac: >> >>> "Warning message: >> >>> In getDependencies(pkgs, dependencies, available, lib) : >> >>> package ‘VariantAnnotation’ is not available (for R version 2.13.2)" >> >>> >> >>> Then, I tried loading the package in Windows that has R version 2.12., >> >>> but >> >>> I the following error message: >> >>> "Warning message: >> >>> In getDependencies(pkgs, dependencies, available, lib) : >> >>> package ‘VariantAnnotation’ is not available" >> >>> >> >>> May I ask you if you know by chance what version of R you were >> running >> >>> for >> >>> the Variant Annotation package? or do you know of any attributes and >> >>> filters in Biomart to get where my variant is located (coding, >> >>> non-coding, >> >>> utr, etc.)? >> >>> >> >>> Thanks, >> >>> >> >>> Adriana >> >>> >> >>> On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain<vobencha@fhcrc.org>> >** >> >> >>> wrote: >> >>> >> >>> Hi Adriana, >> >>>> >> >>>> I believe the filter you want is consequence_type. Take a look at the >> >>>> filters available to you with, >> >>>> >> >>>> listFilters(snpmart) >> >>>> >> >>>> You may also want to take a look at the VariantAnnotation package. >> There >> >>>> are functions >> >>>> >> >>>> ?locateVariants >> >>>> ?predictCoding >> >>>> >> >>>> that can tell you where your variant is located (coding, non- coding, >> >>>> utr, >> >>>> etc.) and provide the amino acid coding change is for the >> non-synonymous >> >>>> variants. Recently SIFT and PolyPhen scores have been made available >> >>>> through db packages >> >>>> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. >> >>>> >> >>>> Valerie >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> On 11/02/2011 07:33 AM, Adriana Munoz wrote: >> >>>> >> >>>> Hello, >> >>>>>> >> >>>>>> I'd like to ask you if there is an attribute to extract SNP >> function >> >>>>>> information from variation datasets in biomaRt such as synonymous, >> >>>>>> nonsynonymous, etc and >> >>>>>> >> >>>>>> a related filter. >> >>>>>> >> >>>>>> I'm using the following rcode: >> >>>>>> >> >>>>>> snpmart = useMart("snp", dataset="hsapiens_snp") >> >>>>> >> >>>>> Any help will be appreciated. >> >>>>> >> >>>>>> Thanks, >> >>>>>> >> >>>>>> Adriana >> >>>>>> >> >>>>>> >> >>>>>> [[alternative HTML version deleted]] >> >>>>>> >> >>>>>> >> >> >> > >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
Hi Xavier, Thanks so much for the information. I'll upgrade my R version to R 2.14, then. Cheers, Adriana On Mon, Nov 14, 2011 at 3:16 AM, Xavier de Pedro <xavier.depedro@vhir.org>wrote: > As far as I remember, only available since R 2.14. > Cheers > Xavier > > > On 11/11/11 18:16, Adriana Munoz wrote: > >> Hi Valerie, >> >> Thanks for the information. I used the filter you mentioned and it works. >> I'd like to try the Variant Annotation package that you mentioned to >> get where my variant is located (coding, non-coding, utr, etc.) , too, but >> I got the following error message in my Mac: >> "Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ‘VariantAnnotation’ is not available (for R version 2.13.2)" >> >> Then, I tried loading the package in Windows that has R version 2.12., but >> I the following error message: >> "Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ‘VariantAnnotation’ is not available" >> >> May I ask you if you know by chance what version of R you were running >> for >> the Variant Annotation package? or do you know of any attributes and >> filters in Biomart to get where my variant is located (coding, non- coding, >> utr, etc.)? >> >> Thanks, >> >> Adriana >> >> On Tue, Nov 8, 2011 at 7:37 PM, Valerie Obenchain<vobencha@fhcrc.org>** >> wrote: >> >> Hi Adriana, >>> >>> I believe the filter you want is consequence_type. Take a look at the >>> filters available to you with, >>> >>> listFilters(snpmart) >>> >>> You may also want to take a look at the VariantAnnotation package. There >>> are functions >>> >>> ?locateVariants >>> ?predictCoding >>> >>> that can tell you where your variant is located (coding, non- coding, utr, >>> etc.) and provide the amino acid coding change is for the non- synonymous >>> variants. Recently SIFT and PolyPhen scores have been made available >>> through db packages >>> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131. >>> >>> Valerie >>> >>> >>> >>> >>> >>> >>> On 11/02/2011 07:33 AM, Adriana Munoz wrote: >>> >>> Hello, >>>>> >>>>> I'd like to ask you if there is an attribute to extract SNP function >>>>> information from variation datasets in biomaRt such as synonymous, >>>>> nonsynonymous, etc and >>>>> >>>>> a related filter. >>>>> >>>>> I'm using the following rcode: >>>>> >>>>> snpmart = useMart("snp", dataset="hsapiens_snp") >>>> >>>> Any help will be appreciated. >>>> >>>>> Thanks, >>>>> >>>>> Adriana >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> > [[alternative HTML version deleted]]
ADD REPLY

Login before adding your answer.

Traffic: 233 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6