tests/testthat/test-enrich.R

In FELLA: Interpretation and enrichment for metabolomics data

context("Enrichment analysis (wrapper enrich)")

# Load data to test
# test.env <- new.env(parent = environment())
test.env <- environment()

test_that("Sample data can be loaded", {
    expect_error({
        data("FELLA.sample", package = "FELLA", envir = test.env)
        data("input.sample", package = "FELLA", envir = test.env)
    }, NA)
})

test_that("Enrichment wrapper", {
    nnodes <- igraph::vcount(getGraph(FELLA.sample))
    npaths <- length(getCom(FELLA.sample, "pathway"))
    
    plyr::l_ply(
        c("hypergeom", "diffusion", "pagerank"), 
        function(method) {
            plyr::l_ply(
                c("normality", "simulation", "t", "gamma"), 
                function(approx) {
                    FELLA.test <- enrich(
                        compounds = input.sample, 
                        methods = method, 
                        approx = approx, 
                        niter = 100, 
                        data = FELLA.sample)
                    
                    expect_s4_class(FELLA.test, "FELLA.USER")
                    
                    pval <- getPscores(FELLA.test, method = method)
                    
                    expect_named(pval)
                    expect_is(pval, "numeric")
                    if (method == "hypergeom") {
                        expect_length(pval, npaths)
                    } else {
                        expect_length(pval, nnodes)
                    }
                    expect_true(all(pval >= 0 & pval <= 1))
                }
            )
        }
    )
})