tests/testthat/test-functions.R

In afukushima/MSEAp: Metabolite Set Enrichment Analysis (MSEA)

context("msea: an R package for metabolite set enrichment analysis (MSEA)")

test_that("read functions", {
    ## read.gpml()
    file <- system.file("extdata", "At_AtMetExpress_overview_WP3622_89229.gpml", 
        package = "MSEAp")
    wikip <- read.gpml(file)
    ## expected values
    expect_equal(wikip[[1]], "WP3622")
    expect_equal(wikip[[2]], "AtMetExpress overview")
    expect_equal(length(wikip[[3]]), 153)
    expect_equal(as.character(wikip[[3]][152]), "24766528")
    
    ## read.gmt()
    file <- system.file("extdata", "sample_SMPDB.gmt", package = "MSEAp")
    smp <- read.gmt(file)
    expect_equal(class(smp), "list")
    expect_equal(length(smp), 10)
    expect_equal(unlist(smp[[10]][1]), "SMP00028")
    expect_equal(unlist(smp[[10]][2]), "Caffeine Metabolism")
    expect_equal(length(unlist(smp[[10]][3])), 24)
    
})

test_that("MSEA calculation", {
    library(MSEApdata)
    data(msea.example)  ## 17 metabolites
    data(mset10hmdb)  ## 10 metabolite-sets
    
    ## MSEA calculation by DEMO datasets
    mset <- mset10hmdb[[4]][[3]]  ## 'GLYCINE, SERINE AND THREONINE METABOLISM'
    mets.refset <- extract.uniq.metabolites(mset10hmdb)
    yy <- length(intersect(mset, msea.example))
    yn <- length(setdiff(mset, msea.example))
    ny <- length(msea.example) - yy
    nn <- length(mets.refset) + yy - length(msea.example) - length(mset)
    
    p.val <- fisher.test(rbind(c(yy, yn), c(ny, nn)), alternative = "greater")$p.value
    
    ## using metaboliteset.enrichment() function
    res <- msea(mset10hmdb, msea.example)
    
    ## expected values
    expect_equal(mset[1], "HMDB00005")
    expect_equal(mset[26], "HMDB06454")
    expect_equal(length(mset), 26)
    expect_equal(length(mets.refset), 174)
    expect_equal(yy, 9)
    expect_equal(yn, 17)
    expect_equal(ny, 8)
    expect_equal(nn, 140)
    expect_equal(p.val, 0.0001054608)
    ## res
    p.val <- round(p.val, digits = 7)
    p.val2 <- as.numeric(as.character(res$p.value[1]))
    expect_true(p.val == p.val2)
    
})