[BioC] ChIPpeakAnno results

[James W. MacDonald]

Hi Marc,

On 8/10/2010 6:26 AM, Marc Noguera wrote:
> Hi all,
> this may be a very naive question by I have been trying to solve it
> myself and i can't get through it.
>
> I have this RangedData object obtained from ChIPpeakAnno Package, which
> correspond toa  Chipseq experiment with annotated peaks, with ENSEMBL
> identificators.
> I can use this output already but like to transform the ENSEMBLID to a
> gene symbol id
>
> for instance: ENSMUSG00000025907 to "Rb1cc1" symbol. It also would be
> useful to add a field linking to a entrez gene web url.
>
> I have been looking at the org.Mm.eg.db package and although I can
> retrieve the symbol for a particular ENSEMBLID can't get it for all the
> elements in the object.

What have you tried so far? Unless you give an example of what you have 
done and how it didn't perform as you expect, it is very difficult for 
anybody to help.

As a shot in the dark, have you looked at the help page for mget()?

I don't really understand how the field linking to Entrez Gene would 
work, considering a RangedData object isn't an HTML page. However, 
building a URL to Entrez Gene isn't that difficult. You can hijack some 
internal code from the annotate package:

 > suppressMessages(library(annotate))
 > egids <- 1:5
 > annotate:::.repositories[["en"]](egids)
[1] 
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=1"
[2] 
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=2"
[3] 
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=3"
[4] 
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=4"
[5] 
"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=5"

But doing it by hand wouldn't be that much more difficult. If you strip 
out the error checking from the above function, all it really consists of is

thefunction <- function(ids){
paste("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=", 

         ids, sep = "")
}

Best,

Jim


>
> Many thanks
> Marc
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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