Hi, I'll get you a step further: On 6/17/12 5:57 PM, "Vincent Carey" <stvjc at="" channing.harvard.edu=""> wrote: >good spec, but i can't get through the whole thing just now. this could >get you started > >source("http://bioconductor.org/biocLite.R") > biocLite("TxDb.Athaliana.BioMart.plantsmart12") >library(TxDb.Athaliana.BioMart.plantsmart12) >txdb = TxDb.Athaliana.BioMart.plantsmart12 >tr = transcriptsBy(txdb, by="gene") # assuming that for each gene's coordinate, you want the extreme starts and ends of its (potentially multiple) transcripts: gene.gr <- reduce(tr) # ISA GenomicRange gene.df<-asgene.gr,'data.frame') # whose names are the gene identifiers Now its a matter of coercing column names, and selecting from the BioMart data just the rows for your identifiers (and checking they are all there, and complaining if not). Cheers, Malcolm Cook > >> tr >GRangesList of length 33602: >$AT1G01010 >GRanges with 1 range and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] 1 [3631, 5899] + | 9694 AT1G01010.1 > >$AT1G01020 >GRanges with 2 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > [1] 1 [5928, 8737] - | 29355 AT1G01020.1 > [2] 1 [6790, 8737] - | 29354 AT1G01020.2 > >$AT1G01030 >GRanges with 1 range and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > [1] 1 [11649, 13714] - | 26358 AT1G01030.1 > >... ><33599 more elements> >--- >seqlengths: > 3 4 1 5 2 Pt Mt > NA NA NA NA NA NA NA > >you could use an org.At* package a bit more simply, use the CHRLOC and >CHRLOCEND >elements. please look at the metadata page of bioconductor.org >INSTALL node for your >organism. this should be a standard use case or faq, perhaps > > > >On Sun, Jun 17, 2012 at 6:33 PM, Josh [guest] ><guest at="" bioconductor.org="">wrote: > >> >> Dear listserv, >> >> I am a long-time R user, novice Bioconductor user. I am quickly >>realizing >> they are not the same thing. I have a very basic question that I hope >>you >> can help me with. >> >> I have a list of genes in Arabidopsis thaliana. I want to input this >>list >> into R/Bioconductor and output a table listing the start and end >>positions >> of each gene. >> >> Specific code that will get the job done will be the most helpful for >>me. >> Also, please tell me the specific packages and databases and such I must >> load into memory. I am a total newbie at this. >> >> Thanks in advance, >> ----------------------------------- >> Josh Banta, Ph.D >> Assistant Professor >> Department of Biology >> The University of Texas at Tyler >> Tyler, TX 75799 >> Tel: (903) 565-5655 >> http://plantevolutionaryecology.org >> >> -- output of sessionInfo(): >> >> > gene.pos <- data.frame(matrix(nrow = 3, ncol = 4)) >> > gene.list <- c("At5g35790", "AT5g60910", "AT1g16560") >> > gene.pos[,1] <- gene.list >> > colnames(gene.pos) <- c("gene", "chromosome", "nuc_sequence_start" , >> "nuc_sequence_end") >> > >> > gene.pos >> gene chromosome nuc_sequence_start nuc_sequence_end >> 1 At5g35790 NA NA NA >> 2 AT5g60910 NA NA NA >> 3 AT1g16560 NA NA NA >> > >> > #now what? How do I fill in the blanks? >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 >> > > [[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