can not link the genomic positions queried and their specific annotation, when getting genomic variants annotated by biomaRt package
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Mao Jianfeng ▴ 290
@mao-jianfeng-3598
Last seen 9.6 years ago
Dear listers, Sean and Steve, I have posted a similar question in this list. But, I am still confused. So I try to describe my question more detail, in order to let it more clear for you. PLEASE read all the 6 sections followed. Thanks a lot. My question is not a student's homework. And, I have only one way to get helps on R and bioconductor. I learned all of them by myself, in a somewhat isolated environment. So, your any helps are very very valuable for me. Jian-Feng, (1) the genomic variants data I need to be annotated: # SNPs,chromosome,start,end SNP_1,1,43,43 SNP_2,2,56,56 (2) I want to get (annotation), there maybe multiples term for a specific annotation column, they need be combined in one cell. Or they need be in different rows of the same column. Whatever they are, the genomic positions should go along with their specific annotations. # SNPs,chromosome,start,end,annotation_term SNP_1,1,43,43,go_1:go_3 SNP_2,2,56,56,go_100:go_1000 or # SNPs,chromosome,start,end,go_term SNP_1,1,43,43,go_1 SNP_1,1,43,43,go_3 SNP_2,2,56,56,go_100 SNP_2,2,56,56,go_1000 (3) It was said that biomaRt package have such functionalities, (4) what I have got using the biomaRt package, library(biomaRt) listMarts() plant = useMart("plant_mart_7") alyr=useDataset("alyrata_eg_gene", mart=plant) atha = useDataset ("athaliana_eg_gene",mart=plant) listAttributes(alyr) listFilters(alyr) chr<-c(rep(1, 10)) start<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000) end<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000) getBM(attributes = c("chromosome_name","start_position","ensembl_gene_id", "go_biological_process_linkage_type"), filters = c("chromosome_name", "start", "end"), values = list(chr, start, end), mart=alyr, uniqueRows = TRUE) (5) what I got chromosome_name start_position end_position ensembl_gene_id 1 1 48875 49123 Al_scaffold_0001_16 2 1 72255 72617 Al_scaffold_0001_21 3 1 10652 11944 Al_scaffold_0001_4 4 1 82573 83367 fgenesh1_pg.C_scaffold_1000018 5 1 87206 90301 fgenesh1_pg.C_scaffold_1000020 6 1 29681 31614 fgenesh1_pm.C_scaffold_1000009 7 1 51526 52636 fgenesh1_pm.C_scaffold_1000016 8 1 78367 80505 fgenesh1_pm.C_scaffold_1000020 9 1 35461 39593 fgenesh2_kg.1__12__AT1G02120.1 10 1 39949 42531 fgenesh2_kg.1__13__AT1G02110.1 11 1 46396 48761 fgenesh2_kg.1__19__AT1G02090.1 12 1 55814 56468 fgenesh2_kg.1__20__AT1G02070.1 13 1 74785 76652 fgenesh2_kg.1__23__AT1G02065.1 14 1 80941 82330 fgenesh2_kg.1__25__AT1G02050.1 15 1 80941 82330 fgenesh2_kg.1__25__AT1G02050.1 16 1 90714 113497 fgenesh2_kg.1__28__AT1G02010.1 17 1 90714 113497 fgenesh2_kg.1__28__AT1G02010.1 18 1 3311 6198 fgenesh2_kg.1__2__AT1G02190.2 19 1 3311 6198 fgenesh2_kg.1__2__AT1G02190.2 20 1 9512 10567 fgenesh2_kg.1__3__AT1G02180.1 21 1 12552 13416 fgenesh2_kg.1__5__AT1G02160.2 22 1 47 2523 scaffold_100001.1 23 1 47 2523 scaffold_100001.1 24 1 7429 7630 scaffold_100003.1 25 1 13702 15386 scaffold_100007.1 26 1 15665 19464 scaffold_100008.1 27 1 19692 20609 scaffold_100009.1 28 1 24515 27497 scaffold_100010.1 29 1 33055 34772 scaffold_100013.1 30 1 33055 34772 scaffold_100013.1 31 1 33055 34772 scaffold_100013.1 32 1 33055 34772 scaffold_100013.1 33 1 33055 34772 scaffold_100013.1 34 1 33055 34772 scaffold_100013.1 35 1 43130 46178 scaffold_100016.1 36 1 49553 51020 scaffold_100018.1 37 1 49553 51020 scaffold_100018.1 38 1 57579 57871 scaffold_100022.1 39 1 58865 72177 scaffold_100023.1 go_biological_process_linkage_type 1 2 3 IEA 4 5 6 7 8 9 10 11 12 13 14 IEA 15 IEA 16 IEA 17 IEA 18 IEA 19 IEA 20 21 22 IEA 23 IEA 24 25 26 IEA 27 28 29 IEA 30 IEA 31 IEA 32 IEA 33 IEA 34 IEA 35 36 IEA 37 IEA 38 39 (6) my problem is I can not link the genomic positions I queried and their specific annotation. -- Jian-Feng, Mao the Institute of Botany, Chinese Academy of Botany,
Annotation GO biomaRt Annotation GO biomaRt • 1.2k views
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@steve-lianoglou-2771
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Hi, On Tue, Feb 8, 2011 at 11:47 AM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: > Dear listers, Sean and Steve, > > I have posted a similar question in this list. But, I am still > confused. So I try to describe my question more detail, in order to > let it more clear for you. PLEASE read all the 6 sections followed. > > Thanks a lot. My question is not a student's homework. And, I have > only one way to get helps on R and bioconductor. I learned all of them > by myself, in a somewhat isolated environment. So, your any helps are > very very valuable for me. > > Jian-Feng, > > > > (1) the genomic variants data I need to be annotated: > # SNPs,chromosome,start,end > SNP_1,1,43,43 > SNP_2,2,56,56 > > (2) I want to get (annotation), there maybe multiples term for a > specific annotation column, they need be combined in one cell. Or they > need be in different rows of the same column. Whatever they are, the > genomic positions should go along with their specific annotations. > > # SNPs,chromosome,start,end,annotation_term > SNP_1,1,43,43,go_1:go_3 > SNP_2,2,56,56,go_100:go_1000 > > or > > # SNPs,chromosome,start,end,go_term > SNP_1,1,43,43,go_1 > SNP_1,1,43,43,go_3 > SNP_2,2,56,56,go_100 > SNP_2,2,56,56,go_1000 > > (3) It was said that biomaRt package have such functionalities, > > (4) what I have got using the biomaRt package, > library(biomaRt) > listMarts() > plant = useMart("plant_mart_7") > alyr=useDataset("alyrata_eg_gene", mart=plant) > atha = useDataset ("athaliana_eg_gene",mart=plant) > > listAttributes(alyr) > listFilters(alyr) > > chr<-c(rep(1, 10)) > start<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000) > end<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000) > > getBM(attributes = > c("chromosome_name","start_position","ensembl_gene_id", > "go_biological_process_linkage_type"), filters = c("chromosome_name", > "start", "end"), values = list(chr, start, end), mart=alyr, uniqueRows > = TRUE) > > (5) what I got > > ? chromosome_name start_position end_position ? ? ? ? ? ? ? ?ensembl_gene_id > 1 ? ? ? ? ? ? ? ?1 ? ? ? ? ?48875 ? ? ? ?49123 ? ? ? ? ? ?Al_scaffold_0001_16 > 2 ? ? ? ? ? ? ? ?1 ? ? ? ? ?72255 ? ? ? ?72617 ? ? ? ? ? ?Al_scaffold_0001_21 > 3 ? ? ? ? ? ? ? ?1 ? ? ? ? ?10652 ? ? ? ?11944 ? ? ? ? ? ? Al_scaffold_0001_4 > 4 ? ? ? ? ? ? ? ?1 ? ? ? ? ?82573 ? ? ? ?83367 fgenesh1_pg.C_scaffold_1000018 > 5 ? ? ? ? ? ? ? ?1 ? ? ? ? ?87206 ? ? ? ?90301 fgenesh1_pg.C_scaffold_1000020 > 6 ? ? ? ? ? ? ? ?1 ? ? ? ? ?29681 ? ? ? ?31614 fgenesh1_pm.C_scaffold_1000009 > 7 ? ? ? ? ? ? ? ?1 ? ? ? ? ?51526 ? ? ? ?52636 fgenesh1_pm.C_scaffold_1000016 > 8 ? ? ? ? ? ? ? ?1 ? ? ? ? ?78367 ? ? ? ?80505 fgenesh1_pm.C_scaffold_1000020 > 9 ? ? ? ? ? ? ? ?1 ? ? ? ? ?35461 ? ? ? ?39593 fgenesh2_kg.1__12__AT1G02120.1 > 10 ? ? ? ? ? ? ? 1 ? ? ? ? ?39949 ? ? ? ?42531 fgenesh2_kg.1__13__AT1G02110.1 > 11 ? ? ? ? ? ? ? 1 ? ? ? ? ?46396 ? ? ? ?48761 fgenesh2_kg.1__19__AT1G02090.1 > 12 ? ? ? ? ? ? ? 1 ? ? ? ? ?55814 ? ? ? ?56468 fgenesh2_kg.1__20__AT1G02070.1 > 13 ? ? ? ? ? ? ? 1 ? ? ? ? ?74785 ? ? ? ?76652 fgenesh2_kg.1__23__AT1G02065.1 > 14 ? ? ? ? ? ? ? 1 ? ? ? ? ?80941 ? ? ? ?82330 fgenesh2_kg.1__25__AT1G02050.1 > 15 ? ? ? ? ? ? ? 1 ? ? ? ? ?80941 ? ? ? ?82330 fgenesh2_kg.1__25__AT1G02050.1 > 16 ? ? ? ? ? ? ? 1 ? ? ? ? ?90714 ? ? ? 113497 fgenesh2_kg.1__28__AT1G02010.1 > 17 ? ? ? ? ? ? ? 1 ? ? ? ? ?90714 ? ? ? 113497 fgenesh2_kg.1__28__AT1G02010.1 > 18 ? ? ? ? ? ? ? 1 ? ? ? ? ? 3311 ? ? ? ? 6198 ?fgenesh2_kg.1__2__AT1G02190.2 > 19 ? ? ? ? ? ? ? 1 ? ? ? ? ? 3311 ? ? ? ? 6198 ?fgenesh2_kg.1__2__AT1G02190.2 > 20 ? ? ? ? ? ? ? 1 ? ? ? ? ? 9512 ? ? ? ?10567 ?fgenesh2_kg.1__3__AT1G02180.1 > 21 ? ? ? ? ? ? ? 1 ? ? ? ? ?12552 ? ? ? ?13416 ?fgenesh2_kg.1__5__AT1G02160.2 > 22 ? ? ? ? ? ? ? 1 ? ? ? ? ? ? 47 ? ? ? ? 2523 ? ? ? ? ? ? ?scaffold_100001.1 > 23 ? ? ? ? ? ? ? 1 ? ? ? ? ? ? 47 ? ? ? ? 2523 ? ? ? ? ? ? ?scaffold_100001.1 > 24 ? ? ? ? ? ? ? 1 ? ? ? ? ? 7429 ? ? ? ? 7630 ? ? ? ? ? ? ?scaffold_100003.1 > 25 ? ? ? ? ? ? ? 1 ? ? ? ? ?13702 ? ? ? ?15386 ? ? ? ? ? ? ?scaffold_100007.1 > 26 ? ? ? ? ? ? ? 1 ? ? ? ? ?15665 ? ? ? ?19464 ? ? ? ? ? ? ?scaffold_100008.1 > 27 ? ? ? ? ? ? ? 1 ? ? ? ? ?19692 ? ? ? ?20609 ? ? ? ? ? ? ?scaffold_100009.1 > 28 ? ? ? ? ? ? ? 1 ? ? ? ? ?24515 ? ? ? ?27497 ? ? ? ? ? ? ?scaffold_100010.1 > 29 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 > 30 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 > 31 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 > 32 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 > 33 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 > 34 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 > 35 ? ? ? ? ? ? ? 1 ? ? ? ? ?43130 ? ? ? ?46178 ? ? ? ? ? ? ?scaffold_100016.1 > 36 ? ? ? ? ? ? ? 1 ? ? ? ? ?49553 ? ? ? ?51020 ? ? ? ? ? ? ?scaffold_100018.1 > 37 ? ? ? ? ? ? ? 1 ? ? ? ? ?49553 ? ? ? ?51020 ? ? ? ? ? ? ?scaffold_100018.1 > 38 ? ? ? ? ? ? ? 1 ? ? ? ? ?57579 ? ? ? ?57871 ? ? ? ? ? ? ?scaffold_100022.1 > 39 ? ? ? ? ? ? ? 1 ? ? ? ? ?58865 ? ? ? ?72177 ? ? ? ? ? ? ?scaffold_100023.1 > ? go_biological_process_linkage_type > 1 > 2 > 3 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? IEA > 4 > 5 > 6 > 7 > 8 > 9 > 10 > 11 > 12 > 13 > 14 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 15 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 16 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 17 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 18 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 19 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 20 > 21 > 22 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 23 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 24 > 25 > 26 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 27 > 28 > 29 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 30 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 31 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 33 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 34 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 35 > 36 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 37 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA > 38 > 39 > > (6) my problem is I can not link the genomic positions I queried and > their specific annotation. I don't understand what you're asking. But, as I pointed out in my original email, your "getBM" call doesn't return any annotations, it only returns the "type" of annotation evidence each gene has. "IEA" tells you what is the source of the annotation you would have received had you included a column for that annotation. You'll note that my first email, I changed your getBM slightly: result <- getBM(attributes=c("chromosome_name","start_position","ensem bl_gene_id", "go_biological_process_linkage_type", "go_biological_process_id"), filters = c("chromosome_name", "start", "end"), values = list(chr, start, end), mart=alyr, uniqueRows = TRUE) See how I added a "go_biological_process_id" as one of the `attributes` to return? You should, too. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Dear Steve, Sorry. My bad english. In short, I have genomic variants (for example SNPs, indels or CNVs), all which were recorded by the specific genomic region (Chromosome, start position, end position). I want to get these genomic variants annotated (this means link each of them to gene, protein, pathway they corresponds to). Can you understand the forward sentences? Steve? If you can not, I want to rewrite what I want to express. Jian-Feng, 2011/2/8 Steve Lianoglou <mailinglist.honeypot at="" gmail.com="">: > Hi, > > On Tue, Feb 8, 2011 at 11:47 AM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: >> Dear listers, Sean and Steve, >> >> I have posted a similar question in this list. But, I am still >> confused. So I try to describe my question more detail, in order to >> let it more clear for you. PLEASE read all the 6 sections followed. >> >> Thanks a lot. My question is not a student's homework. And, I have >> only one way to get helps on R and bioconductor. I learned all of them >> by myself, in a somewhat isolated environment. So, your any helps are >> very very valuable for me. >> >> Jian-Feng, >> >> >> >> (1) the genomic variants data I need to be annotated: >> # SNPs,chromosome,start,end >> SNP_1,1,43,43 >> SNP_2,2,56,56 >> >> (2) I want to get (annotation), there maybe multiples term for a >> specific annotation column, they need be combined in one cell. Or they >> need be in different rows of the same column. Whatever they are, the >> genomic positions should go along with their specific annotations. >> >> # SNPs,chromosome,start,end,annotation_term >> SNP_1,1,43,43,go_1:go_3 >> SNP_2,2,56,56,go_100:go_1000 >> >> or >> >> # SNPs,chromosome,start,end,go_term >> SNP_1,1,43,43,go_1 >> SNP_1,1,43,43,go_3 >> SNP_2,2,56,56,go_100 >> SNP_2,2,56,56,go_1000 >> >> (3) It was said that biomaRt package have such functionalities, >> >> (4) what I have got using the biomaRt package, >> library(biomaRt) >> listMarts() >> plant = useMart("plant_mart_7") >> alyr=useDataset("alyrata_eg_gene", mart=plant) >> atha = useDataset ("athaliana_eg_gene",mart=plant) >> >> listAttributes(alyr) >> listFilters(alyr) >> >> chr<-c(rep(1, 10)) >> start<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000) >> end<-c(33, 999, 3000, 7000, 9000, 10000, 12000, 19000, 80000, 100000) >> >> getBM(attributes = >> c("chromosome_name","start_position","ensembl_gene_id", >> "go_biological_process_linkage_type"), filters = c("chromosome_name", >> "start", "end"), values = list(chr, start, end), mart=alyr, uniqueRows >> = TRUE) >> >> (5) what I got >> >> ? chromosome_name start_position end_position ? ? ? ? ? ? ? ?ensembl_gene_id >> 1 ? ? ? ? ? ? ? ?1 ? ? ? ? ?48875 ? ? ? ?49123 ? ? ? ? ? ?Al_scaffold_0001_16 >> 2 ? ? ? ? ? ? ? ?1 ? ? ? ? ?72255 ? ? ? ?72617 ? ? ? ? ? ?Al_scaffold_0001_21 >> 3 ? ? ? ? ? ? ? ?1 ? ? ? ? ?10652 ? ? ? ?11944 ? ? ? ? ? ? Al_scaffold_0001_4 >> 4 ? ? ? ? ? ? ? ?1 ? ? ? ? ?82573 ? ? ? ?83367 fgenesh1_pg.C_scaffold_1000018 >> 5 ? ? ? ? ? ? ? ?1 ? ? ? ? ?87206 ? ? ? ?90301 fgenesh1_pg.C_scaffold_1000020 >> 6 ? ? ? ? ? ? ? ?1 ? ? ? ? ?29681 ? ? ? ?31614 fgenesh1_pm.C_scaffold_1000009 >> 7 ? ? ? ? ? ? ? ?1 ? ? ? ? ?51526 ? ? ? ?52636 fgenesh1_pm.C_scaffold_1000016 >> 8 ? ? ? ? ? ? ? ?1 ? ? ? ? ?78367 ? ? ? ?80505 fgenesh1_pm.C_scaffold_1000020 >> 9 ? ? ? ? ? ? ? ?1 ? ? ? ? ?35461 ? ? ? ?39593 fgenesh2_kg.1__12__AT1G02120.1 >> 10 ? ? ? ? ? ? ? 1 ? ? ? ? ?39949 ? ? ? ?42531 fgenesh2_kg.1__13__AT1G02110.1 >> 11 ? ? ? ? ? ? ? 1 ? ? ? ? ?46396 ? ? ? ?48761 fgenesh2_kg.1__19__AT1G02090.1 >> 12 ? ? ? ? ? ? ? 1 ? ? ? ? ?55814 ? ? ? ?56468 fgenesh2_kg.1__20__AT1G02070.1 >> 13 ? ? ? ? ? ? ? 1 ? ? ? ? ?74785 ? ? ? ?76652 fgenesh2_kg.1__23__AT1G02065.1 >> 14 ? ? ? ? ? ? ? 1 ? ? ? ? ?80941 ? ? ? ?82330 fgenesh2_kg.1__25__AT1G02050.1 >> 15 ? ? ? ? ? ? ? 1 ? ? ? ? ?80941 ? ? ? ?82330 fgenesh2_kg.1__25__AT1G02050.1 >> 16 ? ? ? ? ? ? ? 1 ? ? ? ? ?90714 ? ? ? 113497 fgenesh2_kg.1__28__AT1G02010.1 >> 17 ? ? ? ? ? ? ? 1 ? ? ? ? ?90714 ? ? ? 113497 fgenesh2_kg.1__28__AT1G02010.1 >> 18 ? ? ? ? ? ? ? 1 ? ? ? ? ? 3311 ? ? ? ? 6198 ?fgenesh2_kg.1__2__AT1G02190.2 >> 19 ? ? ? ? ? ? ? 1 ? ? ? ? ? 3311 ? ? ? ? 6198 ?fgenesh2_kg.1__2__AT1G02190.2 >> 20 ? ? ? ? ? ? ? 1 ? ? ? ? ? 9512 ? ? ? ?10567 ?fgenesh2_kg.1__3__AT1G02180.1 >> 21 ? ? ? ? ? ? ? 1 ? ? ? ? ?12552 ? ? ? ?13416 ?fgenesh2_kg.1__5__AT1G02160.2 >> 22 ? ? ? ? ? ? ? 1 ? ? ? ? ? ? 47 ? ? ? ? 2523 ? ? ? ? ? ? ?scaffold_100001.1 >> 23 ? ? ? ? ? ? ? 1 ? ? ? ? ? ? 47 ? ? ? ? 2523 ? ? ? ? ? ? ?scaffold_100001.1 >> 24 ? ? ? ? ? ? ? 1 ? ? ? ? ? 7429 ? ? ? ? 7630 ? ? ? ? ? ? ?scaffold_100003.1 >> 25 ? ? ? ? ? ? ? 1 ? ? ? ? ?13702 ? ? ? ?15386 ? ? ? ? ? ? ?scaffold_100007.1 >> 26 ? ? ? ? ? ? ? 1 ? ? ? ? ?15665 ? ? ? ?19464 ? ? ? ? ? ? ?scaffold_100008.1 >> 27 ? ? ? ? ? ? ? 1 ? ? ? ? ?19692 ? ? ? ?20609 ? ? ? ? ? ? ?scaffold_100009.1 >> 28 ? ? ? ? ? ? ? 1 ? ? ? ? ?24515 ? ? ? ?27497 ? ? ? ? ? ? ?scaffold_100010.1 >> 29 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 >> 30 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 >> 31 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 >> 32 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 >> 33 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 >> 34 ? ? ? ? ? ? ? 1 ? ? ? ? ?33055 ? ? ? ?34772 ? ? ? ? ? ? ?scaffold_100013.1 >> 35 ? ? ? ? ? ? ? 1 ? ? ? ? ?43130 ? ? ? ?46178 ? ? ? ? ? ? ?scaffold_100016.1 >> 36 ? ? ? ? ? ? ? 1 ? ? ? ? ?49553 ? ? ? ?51020 ? ? ? ? ? ? ?scaffold_100018.1 >> 37 ? ? ? ? ? ? ? 1 ? ? ? ? ?49553 ? ? ? ?51020 ? ? ? ? ? ? ?scaffold_100018.1 >> 38 ? ? ? ? ? ? ? 1 ? ? ? ? ?57579 ? ? ? ?57871 ? ? ? ? ? ? ?scaffold_100022.1 >> 39 ? ? ? ? ? ? ? 1 ? ? ? ? ?58865 ? ? ? ?72177 ? ? ? ? ? ? ?scaffold_100023.1 >> ? go_biological_process_linkage_type >> 1 >> 2 >> 3 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? IEA >> 4 >> 5 >> 6 >> 7 >> 8 >> 9 >> 10 >> 11 >> 12 >> 13 >> 14 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 15 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 16 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 17 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 18 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 19 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 20 >> 21 >> 22 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 23 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 24 >> 25 >> 26 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 27 >> 28 >> 29 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 30 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 31 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 33 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 34 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 35 >> 36 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 37 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?IEA >> 38 >> 39 >> >> (6) my problem is I can not link the genomic positions I queried and >> their specific annotation. > > I don't understand what you're asking. But, as I pointed out in my > original email, your "getBM" call doesn't return any annotations, it > only returns the "type" of annotation evidence each gene has. "IEA" > tells you what is the source of the annotation you would have received > had you included a column for that annotation. > > You'll note that my first email, I changed your getBM slightly: > > result <- getBM(attributes=c("chromosome_name","start_position","ens embl_gene_id", > ?"go_biological_process_linkage_type", "go_biological_process_id"), > ?filters = c("chromosome_name", "start", "end"), > ?values = list(chr, start, end), mart=alyr, uniqueRows = TRUE) > > See how I added a "go_biological_process_id" as one of the > `attributes` to return? You should, too. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- Jian-Feng, Mao the Institute of Botany, Chinese Academy of Botany,
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On Tue, Feb 8, 2011 at 12:54 PM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: > Dear Steve, > > Sorry. My bad english. > > In short, I have genomic variants (for example SNPs, indels or CNVs), > all which were recorded by the specific genomic region (Chromosome, > start position, end position). > > I want to get these genomic variants annotated (this means link each > of them to gene, protein, pathway they corresponds to). > > Can you understand the forward sentences? Steve? If you can not, I > want to rewrite what I want to express. I think I do. Sorry, I didn't mean to imply that I couldn't parse your English, I'm just confused since thought my previous post answers your question. No? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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@steve-lianoglou-2771
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Hi Mao, Please include the bioc mailing list in the cc that you get the best help possible. On Tue, Feb 8, 2011 at 1:10 PM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: > No. > > All your code just return several lines of various attributes (like > defined in biomart), but it is none sense for me. I need my SNPs and > various attributes they correspond to. > > I do not know if biomaRt can do that. > > Please read the simple example followed: > > I have SNPs like this: > # SNPs,chr,start,end > SNP_1,1,43,43 > SNP_2,2,56,56 > > I would want to have annotations like this: > ############################################ > #the chr, start, end here are for my SNPs not for the gos. > ############################################ > # SNPs,chr,start,end,go_term > SNP_1,1,43,43,go_1 > SNP_1,1,43,43,go_3 > SNP_2,2,56,56,go_100 > SNP_2,2,56,56,go_1000 > > Not, just > # chr,start,end,go_term > 1,43,43,go_1 > 1,43,43,go_3 > 2,56,56,go_100 > 2,56,56,go_1000 So ... is the problem that the code I gave you previously gives you "gene-level" annotations, and you want to reassociate them to snps, or what? Search the bioconductor archives for "snp annotation" and you'll find a few things: http://thread.gmane.org/gmane.science.biology.informatics.conductor/32 759/focus=32846 And this might help too: http://thread.gmane.org/gmane.science.biology.informatics.conductor/32 267 If your problem is what I understand it to be, those threads may give you a hint as to how you can use some tools in bioconductor to solve your situation, even though they aren't answers to your *direct* question. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Steve, Sorry for the troubles to you. And, thanks so much for you kindness to me. I do not want to send questions to you directly. Very sorry. I have no reason to do that. Sorry. I can not to hire any bioinformatician. Aslo, I can not hire myself, because I have no money and funding. Though I have not got any training on bioinformatics, in fact I got much from R/bioconductor and also their mailinglist. This is the only way for me to pursuit my research interest. Sorry and Thanks again to you. Best regards, Jian-Feng, 2011/2/9 Steve Lianoglou <mailinglist.honeypot at="" gmail.com="">: > Hi Mao, > > Please include the bioc mailing list in the cc that you get the best > help possible. > > On Tue, Feb 8, 2011 at 1:10 PM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: >> No. >> >> All your code just return several lines of various attributes (like >> defined in biomart), but it is none sense for me. I need my SNPs and >> various attributes they correspond to. >> >> I do not know if biomaRt can do that. >> >> Please read the simple example followed: >> >> I have SNPs like this: >> # SNPs,chr,start,end >> SNP_1,1,43,43 >> SNP_2,2,56,56 >> >> I would want to have annotations like this: >> ############################################ >> #the chr, start, end here are for my SNPs not for the gos. >> ############################################ >> # SNPs,chr,start,end,go_term >> SNP_1,1,43,43,go_1 >> SNP_1,1,43,43,go_3 >> SNP_2,2,56,56,go_100 >> SNP_2,2,56,56,go_1000 >> >> Not, just >> # chr,start,end,go_term >> 1,43,43,go_1 >> 1,43,43,go_3 >> 2,56,56,go_100 >> 2,56,56,go_1000 > > So ... is the problem that the code I gave you previously gives you > "gene-level" annotations, and you want to reassociate them to snps, or > what? > > Search the bioconductor archives for "snp annotation" and you'll find > a few things: > > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 32759/focus=32846 > > And this might help too: > > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 32267 > > If your problem is what I understand it to be, those threads may give > you a hint as to how you can use some tools in bioconductor to solve > your situation, even though they aren't answers to your *direct* > question. > > Hope that helps, > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- Jian-Feng, Mao the Institute of Botany, Chinese Academy of Botany,
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Hi, On Wed, Feb 9, 2011 at 11:45 AM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: > Steve, > > Sorry for the troubles to you. And, thanks so much for you kindness to me. > > I do not want to send questions to you directly. Very sorry. I have no > reason to do that. Sorry. It's fine -- just CC the bioc list so that others can benefit, and the chances of you getting better help in a more timely manner will increase by having more eyeballs see your question. > I can not to hire any bioinformatician. Aslo, I can not hire myself, > because I have no money and funding. > > Though I have not got any training on bioinformatics, in fact I got > much from R/bioconductor and also their mailinglist. This is the only > way for me to pursuit my research interest. Ok, well ... hopefully my previous email has sent you on the right path(?) I do encourage you to read through some of the bioc archives, as other questions might have popped up that are similar. You can get a somehow-usably-searchable version of the mailing list through gmane: http://news.gmane.org/gmane.science.biology.informatics.conductor Best of luck, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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