Passing argument to subset() and unique()

Question

I am using the phyloseq package.

test <- function( ...){

bar <- unique(sampleData[,'pH'])

foo <- subset_samples(phyloseqObject, pH == as.numeric(bar[1]@.Data))
print(foo)

}

test(pH)

I want to pass pH as an argument to test() but unique() won't accept it as valid. I can pass 'pH' to test() but subset_samples() won't accept that as valid. I have tried coercing the argument to several different types with no luck.

SORCE for subset_samples:

subset_samples <- function(physeq, ...){
    if( is.null(sample_data(physeq)) ){ 
        cat("Nothing subset. No sample_data in physeq.\n")
        return(physeq)
    } else {
        oldDF <- as(sample_data(physeq), "data.frame")
        newDF <- subset(oldDF, ...)
        if( class(physeq) == "sample_data" ){
            return(sample_data(newDF))
        } else {
            sample_data(physeq) <- sample_data(newDF)
            return(physeq)
        }
    }
}

@desc That works for `unique()` but I still can't pass to `subset()`. — Alexander, Jan 28 '16 at 00:27

score 1 · Answer 1 · answered Jan 28 '16 at 00:32

1

Try this instead:

test=function(x,...){
   bar=unique(mtcars[,x])
   foo=subset(mtcars,mtcars[,x]==bar[1])
   return(foo)
}

answered Jan 28 '16 at 00:32

desc

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But that `subset()` call goes through `subset_samples()` in my case and that function wants a logical expression. I need to use it that way because of the way the phyloseq-class is built. – Alexander Jan 28 '16 at 00:43
Added source to `subset_samples()` for clarity. – Alexander Jan 28 '16 at 00:50
1

I finally figured it out. Thank you for pointing me in the right direction. – Alexander Jan 28 '16 at 01:51
great! glad to help! – desc Jan 28 '16 at 03:45

Alexander · Accepted Answer · 2016-01-28T01:48:55.270

0

Building on what @desc said I managed to solve it like this:

test <- function(...){

    bar <- unique(sampleData[,...])

    foo <- subset_samples(phyloseqObject, eval(parse(bar@names)) == as.numeric(bar[1]))
    print(foo)

}

test('pH')

edited Jan 28 '16 at 01:48

answered Jan 28 '16 at 01:24

Alexander

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Passing argument to subset() and unique()

2 Answers2