[BioC] Getting the start and end positions of a list of genes

[Josh [guest]]

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?

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