Question

I am writing a function foo(…, lev) on the base of makeContrasts function of package limma (of bioconductor):

makeContrasts(..., contrasts=NULL, levels)

I want to pass the … argument of foo ‘as-is’ to makeContrasts. Here is my code:

foo = function(..., lev) {
    e = substitute(list(...))
    makeContrasts(e[[2]], levels=lev)
}

foo(a + b, design)

The reason I have used e[[2]] is that e will be list(a+b) and e[[1]] is list but e[[2]] is what I need: a + b

But the problem is that the actual argument passed to makeContrast is e[[2]] and not a + b.
So what to do?

The complete parameter assignments are as below:

ct = factor(c("a","b"))
design = model.matrix(~0+ct)
colnames(design)=levels(ct)
makeContrasts(a+b,levels=design) # It works
foo(a+b, design) # Does not work

Answer 1

A may be over simplifying the problem, but does the following not just work

foo = function(..., lev) {
 makeContrasts(...,levels =lev)
}

foo(a + b,b+c, lev =letters[1:3])


## Contrasts
## Levels a + b b + c
## a     1     0
## b     1     1
## c     0     1

using your example

I don’t appear to be oversimplifying.

If ... contain the arguments to be passed to another function, then all you need is to pass ... to that function. ...

ct = factor(c("a","b"))
design = model.matrix(~0+ct)
colnames(design)=levels(ct)
makeContrasts(a+b,levels=design) 
## Contrasts
## Levels a + b
##  a     1
##  b     1
foo(a+b, lev = design)
## Contrasts
## Levels a + b
##  a     1
##  b     1