Turn string into the contents of a function in R for pipeline

Question

I have am using the makeContrasts function as part of a pipeline (with limma). I have several studies, which are entered into the pipeline one after the other. For two of which, the makeContrasts functions looks like this:

aarts_1_cm = makeContrasts(R10d = labelR - labelP,
                           R1nMRap = labelR1 - labelP,
                           R10nMRap_OSKM = labelR10 - labelO,
                           levels = Design)

and

aarts_2_cm = makeContrasts(OSKM14 = labelO14 - labelP14,
                           OSKM14mTORsh_OSKM14p21sh = labelOT14 - labelOp14,
                           OSKM20mTORsh_OSKM20p21sh = labelOT20 - labelOp20,
                           levels = Design)

As the contrasts are different for each study, I cannot incorporate them into the pipeline. I have therefore turned the contents of the function into a string:

aarts_2 = "OSKM14 = labelO14 - labelP14,
                           OSKM14mTORsh_OSKM14p21sh = labelOT14 - labelOp14,
                           OSKM20mTORsh_OSKM20p21sh = labelOT20 - labelOp20,
                           levels = Design"

So that I can then do makeContrasts(unstring(aarts_2)), but I don't know how to unstring aarts_2 so that the function will read it. Or if there is a better way to do this. I would appreciate any help with this.

Thanks.

score 2 · Accepted Answer · answered Apr 06 '20 at 17:56

I don't think there's a way to write the unstring function you want, but you can do this:

makeContrastsFromString <- function(s)
  eval(parse(text = paste("makeContrasts(", s, ")")))

then

makeContrastsFromString(aarts_2)

should give you want you want. I haven't tested it, since I can't install limma to get makeContrasts. My function is pretty fragile; if a user breaks up the lines into separate elements of a string vector, it won't work. I'll leave it to you to make it robust against that kind of thing.

Turn string into the contents of a function in R for pipeline

1 Answers1