Tim et al., > library(annotate) > map <- getAnnMap("SYMBOL", "hgu95av2") might be a more robust solution, e.g., doing the paste, loading the package if it is not already, choosing the '.db' version of the annotation package in preference to the environment-based version, etc. There's also a fun function 'revmap' which I find quite useful and amazingly fast for reversing the map (e.g., from SYMBOL to probe, instead of probe to SYMBOL). > rmap <- revmap(map) > mget(head(ls(rmap)), rmap) $`15E1.2` [1] "34083_at" $`2'-PDE` [1] "38144_at" $`3.8-1` [1] "34934_at" $`76P` [1] "40986_s_at" "40985_g_at" "40984_at" $AADAC [1] "36512_at" $AAK1 [1] "40628_at" "40572_at" "34949_at" "39456_at" "39463_at" Martin Tim Smith <tim_smith_666 at="" yahoo.com=""> writes: > Thanks Sean & Marc. That did it! > > > > ----- Original Message ---- > From: Marc Carlson <mcarlson at="" fhcrc.org=""> > To: Tim Smith <tim_smith_666 at="" yahoo.com=""> > Cc: bioc <bioconductor at="" stat.math.ethz.ch=""> > Sent: Monday, March 3, 2008 12:53:10 PM > Subject: Re: [BioC] passing in parameters to annotation packages (e.g hgu95av2) > > Tim Smith wrote: >> Hi, >> >> I was trying to pass in a parameter (on the fly), but am unable to figure out how to get what I want. Here is what I want: >> >> xx <- as.list(hgu95av2SYMBOL) >> >>> length(xx) >>> >> [1] 12625 >> >> However, when I try to build the string on the fly and pass it as a parameter, for example: >> >> >>> var <- 'hgu95av2' >>> tempVar <- paste(var,'SYMBOL',sep='') >>> yy <- as.list(tempVar) >>> length(yy) >>> >> [1] 1 >> >>> tempVar >>> >> [1] "hgu95av2SYMBOL" >> >> >> I understand that in the second case, I have just created a string and the results are not surprising!. But how do I get it to do what I really want? >> >> >> >> >> >> >> >> _____________________________________________________________ _______________________ >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > Hi Tim, > > I think that the function you want to use is get(). > > So for your example: > > var <- 'hgu95av2' > tempVar <- paste(var,'SYMBOL',sep='') > > #just add this function call into your flow to find the variable that > you seek > #(instead of the string which as you mentioned will NOT be what you want): > foo = get(tempVar) > > yy = as.list(foo) > length(yy) > > #Which gives the answer that I think you wanted: [1] 12625 > > > Let me know if this doesn't help, > > > Marc > > > > > > > ______________________________________________________________ ______________________ > Be a better friend, newshound, and > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793