Make sure a data frame has been "fun through" a function

Stray attributes on data.frames may or may not survive some simple
operations on the data.frame.  E.g.,

d <- data.frame(X=1:5, Y=log(1:5), G=factor(rep(c("a","b"),c(2,3))))
attr(d, "checked") <- TRUE
wasChecked <- function(x) isTRUE(attr(x, "checked"))
wasChecked(d)

[1] TRUE

wasChecked(d[1:4,]) # select some rows

[1] TRUE

wasChecked(d[,1:2]) # select some columns

[1] FALSE

d[1,1] <- 10 # change a single value
wasChecked(d)

[1] TRUE

d$NewColumn <- 11:15 # add a column
wasChecked(d)

[1] TRUE

I don't know if this would be an issue in your case.  If it is, you
could subclass "data.frame" and define methods so that the operations
of interest preserve or remove the attribute in the way that you
desire.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Tue, Feb 21, 2017 at 8:30 AM, Charles C. Berry <ccberry at ucsd.edu>
wrote:

On Tue, 21 Feb 2017, stephen sefick wrote:

Sorry for not being clear. I have never used S3 methods before. Below is
some R code that sketches out my idea. Is this a sensible solution?

Sure. See comments (untested) inline.

Chuck

test_data <- data.frame(a=1:10, b=1:10, c=1:10)

functionA <- function(x, impossible_genotype){
   ##some data processing
   y <- x

   ##return S3 to be able to use impossible genotype later
   class(y) <- append(class(y),"genotypes")

     class(y) <- c("genotypes",class(y))

   attr(y, "impossible_genotype") <- impossible_genotype

   return(y)
}

test_data_genotypes <- functionA(test_data, impossible_genotype="Ref")

functionB <- function(x){
   ##stop if pre-processed with functionA
   if(sum(class(x)=="genotypes")!=1){stop("Need to pre-process data

with

functionA")}

    if(!(inherits("genotypes")){
        stop("Need to pre-process data with functionA")}


or in functionA you could skip the class()<- and just set the
"impossible_genotypes" attribute to FALSE when there are none such.

Then here test

     if (is.null(attr(x,"impossible_genotypes"))){
                stop("Need to pre-process data with functionA")
        } else {
                return(alleles)
        }

   ##use this later in functionB to
   impossible_genotype <- attributes(x)$impossible_genotype

     impossible_genotype <- attr(x,"impossible_genotype")

   alleles <- c("Ref", "Alt")

   coded_genotype <- alleles[alleles!=impossible_genotype]

     maybe `!is.element(alleles,impossible_genotype)' is safer than `!='

   return(coded_genotype)
}

##stop if not pre-processed with functionA
functionB(test_data)

##processed with functionA
functionB(test_data_genotypes)

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