tests/testthat/test_metabData.R

In hhabra/metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

###############################################
# Tests for the metabData object and methods
###############################################

context("metabData tests")

test_that("field detection tests",{
    data("plasma20")

    p20 <- metabData(plasma20, samples = "Red", extra = "CHEAR")

    testthat::expect_length(getSamples(p20), 5)
    testthat::expect_length(getExtra(p20), 5)
    testthat::expect_false(any(getSamples(p20) %in% getExtra(p20)))

    data <- getData(p20)
    testthat::expect_equal(nrow(plasma20), nrow(data))

    p20_2 <- metabData(plasma20, samples = "RedCross", extra = "CH")
    testthat::expect_equivalent(p20, p20_2)

    plasma20$rt[25] <- plasma20$rt[25] * -1
    testthat::expect_error(metabData(plasma20, samples = "RedCross", extra = "CHEAR"))

    plasma20$rt[25] <- plasma20$rt[25] * -10000
    testthat::expect_warning(metabData(plasma20, samples = "RedCross", extra = "CHEAR"))

    plasma20$rt[25] <- plasma20$rt[25] * 1/10000
    plasma20$mz[3] <- plasma20$mz[3] * 100
    testthat::expect_warning(metabData(plasma20, samples = "RedCross", extra = "CHEAR"))

    plasma20$mz[3] <- plasma20$mz[3] / 100
    p20 <- suppressWarnings(metabData(plasma20))
    testthat::expect_equivalent(grep("POOL|CHEAR|Red|Bl", names(plasma20), value = TRUE),
                      getSamples(p20))

    testthat::expect_error(metabData(plasma20, mz = "mz", rt = "mz"))
    testthat::expect_error(metabData(plasma20, rt = "id"))
})

test_that("RT filtering test", {
    data("plasma20")
    p20 <- metabData(plasma20, samples = "CHEAR", misspc = 15, rtmax = 17.25)

    testthat::expect_lt(max(getData(p20)[["rt"]]), 17.25)
    testthat::expect_gt(getStats(p20)[["filtered_by_rt"]], 0)
})


test_that("filter_missingness test", {
    data("plasma20")

    plasma20[["CHEAR.20min.2"]] <- NA
    plasma20[["CHEAR.20min.2"]][100] <- 1000

    p20 <- metabData(plasma20, samples = "CHEAR", misspc = 15)

    testthat::expect_equal(getStats(p20)[["final_count"]], 1)

})

test_that("filter_duplicates test", {
    mz <- seq(100, 110, 0.01)
    rt <- rep(10,1001)
    s <- seq(1001.1,1.1, -1)
    data <- data.frame(mz = mz, rt = rt, s = s)
    md <- suppressWarnings(metabData(data, duplicate = c(0.01,0.01)))
    testthat::expect_equal(getStats(md)[["filtered_as_duplicates"]], 500)
})

test_that("merge_duplicates test", {
    mz <- seq(100.01, 110, 0.01)
    rt <- rep(10,1000)
    id <- rep(c("a","b"), 500)
    s <- rep(c(2,1,1,0), 250)
    data <- data.frame(id = id, mz = mz, rt = rt, s = s)
    od <- opts.duplicate(0.01, 0.01, "merge")
    md <- suppressWarnings(metabData(data, duplicate = od))
    d <- getData(md)
    testthat::expect_equal(sum(d[["s"]]), 750)
    testthat::expect_equal(unique(d[["id"]]), "{a; b}")
})