tests/testthat/test_getMt.R

In LiesaSalzer/mobilityTransformationR: Effective mobility scale transformation of CE-MS(/MS) data

## load toy example data set
fl <- system.file("CE-MS/CEMS_10ppm.mzML",
    package = "msdata"
)
raw_data <- MSnbase::readMSData(
    files = fl,
    mode = "onDisk"
)
# [M+H]+ of paracetamol: mz = 152.071154
mz_paracetamol <- c(152.065154, 152.076154)
mt_paracetamol <- c(600, 900)


test_that("Getting migration time works", {
    mt <- getMtime(raw_data,
        mz = mz_paracetamol,
        mt = mt_paracetamol
    )
    expect_true(is.data.frame(mt))
    expect_equal(colnames(mt), c("rtime", "fileIdx"))
    expect_equal(dim(mt), c(1, 2))
    expect_true(is.numeric(mt$rtime))
    expect_true(is.numeric(mt$fileIdx))
    expect_equal(mt[1, 1], 840.796, tolerance = 1e-06)
    expect_equal(mt[1, 2], 1)

    expect_error(
        getMtime(NA, mz = mz_paracetamol, mt = mt_paracetamol),
        "'x' is not of class 'OnDiskMSnExp'!"
    )
    expect_error(
        getMtime(raw_data, mz = mz_paracetamol),
        "Arguments 'mz' and 'mt' are required!"
    )
    expect_error(
        getMtime(raw_data, mt = mt_paracetamol),
        "Arguments 'mz' and 'mt' are required!"
    )
    expect_error(
        getMtime(raw_data,
            mz = c(150, 152.1),
            mt = mt_paracetamol
        ),
        "2 peaks have been found in file 1, align input parameters"
    )
    expect_warning(expect_error(
        getMtime(raw_data,
            mz = c(150.001, 150.002),
            mt = mt_paracetamol
        ),
        "0 peaks have been found in file 1, align input parameters"
    ))
})

test_that("Getting migration time with CentWaveParam works", {
    mt_cwp <- getMtime(raw_data,
        mz = c(152, 152.2),
        mt = mt_paracetamol,
        param = xcms::CentWaveParam()
    )

    expect_true(is.data.frame(mt_cwp))
    expect_equal(colnames(mt_cwp), c("rtime", "fileIdx"))
    expect_equal(dim(mt_cwp), c(1, 2))
    expect_true(is.numeric(mt_cwp$rtime))
    expect_true(is.numeric(mt_cwp$fileIdx))
    expect_equal(mt_cwp[1, 1], 841.305, tolerance = 1e-06)
    expect_equal(mt_cwp[1, 2], 1)

    expect_error(
        getMtime(NA, mz = mz_paracetamol, mt = mt_paracetamol),
        "'x' is not of class 'OnDiskMSnExp'!"
    )
    expect_error(
        getMtime(raw_data, mz = mz_paracetamol),
        "Arguments 'mz' and 'mt' are required!"
    )
    expect_error(
        getMtime(raw_data, mt = mt_paracetamol),
        "Arguments 'mz' and 'mt' are required!"
    )
    expect_error(
        getMtime(raw_data,
            mz = c(150, 152.1),
            mt = mt_paracetamol
        ),
        "2 peaks have been found in file 1, align input parameters"
    )
    expect_warning(expect_error(
        getMtime(raw_data,
            mz = c(150.001, 150.002),
            mt = mt_paracetamol
        ),
        "0 peaks have been found in file 1, align input parameters"
    ))
})