passing arguments to subset from a function

argument which I will pass on to subset() somewhere inside my function.  

I would use the example of .() function from plyr package in this case:

.<-function (...){
     structure(as.list(match.call()[-1]), class = "quoted")
}

myfunction<-function(table, extraction)  {
     table2<-subset(table, eval(extraction[[1]]))
     return(table2)
 }
myfunction(iris, extraction = .(Species=="setosa"))

You can pass as many arguments in .() as you wish and index correspondingly in myfunction afterwards.

HTH.