Hi Georg -- Saroj K Mohapatra wrote: > Hi Georg: > > It is doable, the idea is to create the command string first and then > evaluate it as an R expression. > > Frirst, collapse the contrasts. If it is a vector like in your case: > > a<-c("B-A","C-B","C-A") > > > astr=paste(a, collapse=",") > > astr > [1] "B-A,C-B,C-A" > > Then add correct strings before and after. > > prestr="makeContrasts(" > > poststr=",levels=design)" > > commandstr=paste(prestr,astr,poststr,sep="") > > commandstr > [1] "makeContrasts(B-A,C-B,C-A,levels=design)" > > Now evaluate the command string: > > eval(parse(text=commandstr)) > Contrasts > Levels B - A C - B C - A > A -1 0 -1 > B 1 -1 0 > C 0 1 1 > > However, 'eval' is a tricky thing (see some comments here on the list > some days back). There might be better (i.e., more straight-forward) > ways of doing this. Hopefully, others would comment. > > Best wishes, > > Saroj > > Georg Otto wrote: >> Hi, >> >> maybe this is a more general R programming question, but I first try it >> here, because the problem occured to me with limma: >> >> I use the function makeContrasts >> >> makeContrasts(...,levels=design) >> >> like this >> >> makeContrasts(B-A,C-B,C-A,levels=design) >> >> >> now instead of giving explicitely "B-A,C-B,C-A" I would like to replace >> this by a variable, eg: >> >> a<-c("B-A","C-B","C-A") >> >> makeContrasts(a,levels=design) >> >> unfortunately, this does not work. One way is to aim for do.call(makeConstrasts, myargs) where the 'myargs' is a list that you can construct any way you like, e.g., myargs = list("B-A", "C-B", "C-A", levels=design) do.call(makeContrasts, myargs) Martin >> >> So my question is: how can I make this work, and - more generally - how >> can I replace the "..." option in a function by a variable? >> >> Thanks, >> >> Georg >> >> _______________________________________________ >> 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 >> >> > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 M1 B861 Phone: (206) 667-2793

Georg Otto wrote: > Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > >>> Georg Otto wrote: >>>> Hi, >>>> >>>> maybe this is a more general R programming question, but I first try it >>>> here, because the problem occured to me with limma: >>>> >>>> I use the function makeContrasts >>>> >>>> makeContrasts(...,levels=design) >>>> >>>> like this >>>> >>>> makeContrasts(B-A,C-B,C-A,levels=design) >>>> >>>> >>>> now instead of giving explicitely "B-A,C-B,C-A" I would like to replace >>>> this by a variable, eg: >>>> >>>> a<-c("B-A","C-B","C-A") >>>> >>>> makeContrasts(a,levels=design) >>>> >>>> unfortunately, this does not work. >> One way is to aim for >> >> do.call(makeConstrasts, myargs) >> >> where the 'myargs' is a list that you can construct any way you like, e.g., >> >> myargs = list("B-A", "C-B", "C-A", levels=design) >> do.call(makeContrasts, myargs) >> > > thanks a lot, that helps, but there comes up another problem: > > I start with a character vector, from which I have to construct the > list: > >> contrast.vector > [1] "First=B-A" "Second=D-C" I'm not sure that you want to start from there? myargs <- list(First="B-A", Second="D-C") or x <- c("First=B-A", "Second=D-C") namecontr <- strsplit(x, "=") myargs <- lapply(namecontr, "[[", 2) names(myargs) <- sapply(namecontr, "[[", 1) myargs[["levels"]] <- design but I wonder a bit what the 'bigger picture' is, since these kinds of manipulations are not what one would do in a typical analysis. Martin > > How do I get from there to: > > myargs = list(First="B-A", Second="D-C", levels=design) > > Any hint will be appreciated, > > Georg > > _______________________________________________ > 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