After some searching and reading of old post (subsetting SummarizedExperiments - a proposal (or a hack?)) I am wondering if there exist a manner in which SummarizedExperiment objects can be subset by metadata with an explicit method beyond [. To illustrate, I have a small example:

This is possible with the bracket method:

library(HMP16SData)
V13 <- V13()
V13[, V13$hmp_body_subsite == "Stool"]

But I have something in mind like this:

library(HMP16SData)
V13 <- V13()
subset(V13, V13$hmp_body_subsite == "Stool")

I have looked at subset in SummarizedExperiment and FilterRules in S4Vectors but don't yet have a clear idea how this might be accomplished. Any idea would be helpful, thanks!

Try

V13 <- as(V13, "RangedSummarizedExperiment")
subset(V13, select = hmb_body_subsite == "Stool")

Actually the coercion seems to be a hack; I'm not sure why there is  no subset,SummarizedExperiment-method; an implementation might be

setMethod("subset", "SummarizedExperiment",
    function(x, subset, select, ...)
{
    i <- S4Vectors:::evalqForSubset(subset, rowData(x), ...)
    j <- S4Vectors:::evalqForSubset(select, colData(x), ...)
    x[i, j]
})

Thank you Martin. Even with subset(V13, select = V13$hmp_body_subsite == "Stool") there is still an error with the coercion but once the method is there then the behavior is as expected. I will add this a pull request against SummarizedExperiment on GitHub.