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,

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,