[BioC] variable as argument to makeContrasts (limma)

[Martin Morgan]

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