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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