Thanks a lot. Steve. You have given me a good guide. Jian-Feng, 2011/2/8 Steve Lianoglou <mailinglist.honeypot at="" gmail.com="">: > Hi, > > On Tue, Feb 8, 2011 at 9:24 AM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: >> Dear Steve, >> >> Thanks for your kindness. Could you please give me more directions on >> this annotation problem? >> >> ######################### >> (1) >> ######################### >> I want each my SNP has just one line of annotation in separate >> columns. If there are the multiple terms for the same attributes (for >> example, multiple go terms are shared at that location), I would like >> to include them in the same column with symbols (such ; ?: ?| ) >> separated each of them. >> >> for example I have SNPs like this: >> # SNPs,chr,start,end >> SNP_1,1,43,43 >> SNP_2,2,56,56 >> >> I would have annotations like this: >> # SNPs,chr,start,end,go_term >> SNP_1,1,43,43,go_1:go_3 >> SNP_2,2,56,56,go_100:go_1000 > > I'll give you this one ... continuing from my previous example: say > the getBM call stores its return value in `result`: > > library(plyr) > summary <- ddply(result, .(chromosome_name, start_position), function(x) { > ?new.x <- x[1,] > ?new.x$go_biological_process_id <- paste(x$go_biological_process_id, > collapse="|") > ?new.x > }) > > I'll leave the rest as an exercise for you. > > -steve > > >> >> ######################### >> (2) >> ######################### >> Alternatively, I would like to have the SNPs position be combined with >> its annotations results, so as to know which the annotation lines are >> corresponding to. I do not know how to do that using bioconductor >> packages. Look the example followed: >> >> for example I have SNPs like this: >> # SNPs,chr,start,end >> SNP_1,1,43,43 >> SNP_2,2,56,56 >> >> I would have annotations like this: >> # 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 >> >> Jian-Feng, >> >> 2011/2/8 Steve Lianoglou <mailinglist.honeypot at="" gmail.com="">: >>> Hi, >>> >>> On Tue, Feb 8, 2011 at 5:49 AM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: >>>> Dear listers, >>>> >>>> I am new to bioconductor. >>>> >>>> I have genomic variations (SNP, indel, CNV) coordinated by >>>> chromosome:start:end in GFF/BED/VCF format. One genomic variation is >>>> defined a specific genomic position (in base pair). >>>> >>>> for example: >>>> # SNPs,chr,start,end >>>> SNP_1,1,43,43 >>>> SNP_2,2,56,56 >>>> >>>> I would like to get such genomic variations annotated by various >>>> gen/protein/passway centric annotations (as listed in BioMart >>>> databases). I tried R/bioconductor biomaRt package. But, I failed to >>>> get a unique line of annotation for a specific genomic position. Could >>>> you please give any directions on that? >>> >>> Could you explain a bit more about what you mean when you say "get a >>> unique line of annotation"? >>> >>> The only informative info `getBM` query is returning is the gene id >>> for the location, and the GO term evidence code >>> (go_biological_process_linkage_type). If you add, say, >>> "go_biological_process_id", you get the biological go terms associated >>> with the position, ie: >>> >>> result <- getBM(attributes=c("chromosome_name","start_position","e nsembl_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) >>> >>> If you problem is that some positions have more than one row, like so: >>> >>> chromosome_name start_position ? ? ensembl_gene_id ?... >>> go_biological_process_id >>> ? ? ? ? ? ? ?1 ? ? ? ? ?33055 ? scaffold_100013.1 >>> GO:0006355 >>> ? ? ? ? ? ? ?1 ? ? ? ? ?33055 ? scaffold_100013.1 >>> GO:0006886 >>> ? ? ? ? ? ? ?1 ? ? ? ? ?33055 ? scaffold_100013.1 >>> GO:0006913 >>> ? ? ? ? ? ? ?1 ? ? ? ? ?33055 ? scaffold_100013.1 >>> GO:0007165 >>> ? ? ? ? ? ? ?1 ? ? ? ? ?33055 ? scaffold_100013.1 >>> GO:0007264 >>> >>> this happens because multiple go terms are shared at that location. If >>> you want to just pick one, but you'll have to decide how you want to >>> do that. >>> >>> If you want to somehow summarize each chromosome/start_position into >>> one row, you can iterate over the data by this combination easily >>> with, say, the ddply function from the plyr package: >>> >>> library(plyr) >>> summary <- ddply(result, .(chromosome_name, start_position), function(x) { >>> ?# x will have all of the rows for a given chromosome_name / start_position >>> ?# combo. We can arbitrarily just return the first row, but you'll likely >>> ?# want to do something smarter: >>> ?x[1,] >>> }) >>> >>> If you look at `summary`, you'll have one row per position. >>> >>> -- >>> 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 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,