tests/testthat/test_functions-xcmsSwath.R

In sneumann/xcms: LC-MS and GC-MS Data Analysis

test_that(".which_mz_in_range works", {
    skip_on_os(os = "windows", arch = "i386")

    mz <- 3.4
    lowerMz <- c(1, 3, 8, 12)
    upperMz <- c(3, 7, 11, 15)
    res <- .which_mz_in_range(mz, lowerMz, upperMz)
    expect_equal(res, 2L)
    res <- .which_mz_in_range(c(3, 3.4, 9), lowerMz, upperMz)
    expect_equal(res, list(c(1L, 2L), 2L, 3L))
})

test_that(".which_chrom_peak_overlap_rt works", {
    skip_on_os(os = "windows", arch = "i386")

    pks <- cbind(rtmin = c(1, 2, 3, 4, 5), rtmax = c(2, 3, 4, 5, 6))
    res <- .which_chrom_peak_overlap_rt(c(rtmin = 1.1, rtmax = 2.2), pks)
    expect_equal(res, c(1L, 2L))
    res <- .which_chrom_peak_overlap_rt(c(rtmin = 3.1, rtmax = 3.2), pks)
    expect_equal(res, 3L)
})

test_that(".which_chrom_peak_diff_rt works", {
    skip_on_os(os = "windows", arch = "i386")

    pks <- cbind(rt = c(1, 2, 3, 4, 5), rtmax = c(2, 3, 4, 5, 6))
    res <- .which_chrom_peak_diff_rt(c(rt = 1.1), pks, diffRt = 2)
    expect_equal(res, c(1L, 2L, 3L))
    res <- .which_chrom_peak_diff_rt(c(rt = 3.1), pks, diffRt = 0.101)
    expect_equal(res, 3L)
})

test_that(".reconstruct_dia_ms2 works", {
    res <- .reconstruct_dia_ms2(pest_swth)
    expect_true(is(res, "Spectra"))
    expect_equal(length(res), nrow(chromPeaks(pest_swth, msLevel = 1L)))
    expect_equal(res$peak_id, rownames(chromPeaks(pest_swth, msLevel = 1L)))
    expect_equal(
        res$precursorMz, unname(chromPeaks(pest_swth, msLevel = 1L)[, "mz"]))
})

test_that(".reconstruct_dia_ms2 works", {
    res <- .reconstruct_dia_ms2(pest_swth)
    expect_true(is(res, "Spectra"))
    expect_equal(length(res), nrow(chromPeaks(pest_swth, msLevel = 1L)))
    expect_equal(res$peak_id, rownames(chromPeaks(pest_swth, msLevel = 1L)))
    expect_equal(
        res$precursorMz, unname(chromPeaks(pest_swth, msLevel = 1L)[, "mz"]))
})