## create test sets for test_function_Spectra_metrics.R
## create toy example data set
fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
sps_sciex <- Spectra(fls, backend = MsBackendMzR())
set.seed(1)
## add some fake charges
sps_sciex@backend$precursorCharge <- as.integer(
sample(x = c(1, 2, 3, 4), size = 1862,
replace = TRUE, prob = c(0.7, 0.15, 0.1, 0.05)))
## add some fake precursorMZ
sps_sciex@backend$precursorMz <- rnorm(n = 1862, mean = 500, sd = 100)
## add some fake precursorIntensity
sps_sciex@backend$precursorIntensity <- rpois(n = 1862, lambda = 10000)
## START unit test rtDuration ##
test_that("rtDuration", {
expect_error(rtDuration(NULL), "unable to find an inherited method")
expect_error(rtDuration(NULL), "unable to find an inherited method")
expect_equal(rtDuration(sps_sciex), 259.482)
})
## END unit test rtDuration ##
## START unit test rtOverTicQuantile ##
test_that("rtOverTicQuantile", {
expect_error(rtOverTicQuantile(NULL), "unable to find an inherited method")
expect_error(rtOverTicQuantile(NULL), "unable to find an inherited method")
suppressWarnings(tmp <- rtOverTicQuantile(sps_sciex))
expect_equal(as.numeric(tmp),
c(0.0, 0.25, 0.5, 0.75, 1), tolerance = 1e-02)
expect_equal(names(tmp), c("0%", "25%", "50%", "75%", "100%"))
})
## END unit test rtOverTicQuantile ##
## START unit test rtOverMsQuarters ##
test_that("rtOverMsQuarters", {
expect_error(rtOverMsQuarters(NULL), "unable to find an inherited method")
expect_error(rtOverMsQuarters(NULL), "unable to find an inherited method")
expect_equal(as.numeric(rtOverMsQuarters(sps_sciex, msLevel = 1L)),
c(0.25, 0.5, 0.75, 1), tolerance = 1e-02)
expect_equal(names(rtOverMsQuarters(sps_sciex, msLevel = 1L)),
c("Quarter1", "Quarter2", "Quarter3", "Quarter4"), tolerance = 1e-06)
expect_error(rtOverMsQuarters(sps_sciex, msLevel = 2L),
"'spectra' does contain less than four spectra")
})
## END unit test rtOverMsQuarters ##
## START unit test ticQuantileToQuantileLogRatio ##
test_that("ticQuantileToQuantileLogRatio", {
expect_error(ticQuantileToQuantileLogRatio(NULL),
"unable to find an inherited method")
expect_error(ticQuantileToQuantileLogRatio(NULL),
"unable to find an inherited method")
tmp <- suppressWarnings(ticQuantileToQuantileLogRatio(sps_sciex,
relativeTo = "previous", msLevel = 1L))
expect_equal(as.numeric(tmp), c(-0.05853477, -0.58202994, 0.15361253))
expect_equal(names(tmp), c("Q2/Q1", "Q3/Q2", "Q4/Q3"))
tmp <- suppressWarnings(ticQuantileToQuantileLogRatio(sps_sciex,
relativeTo = "Q1", msLevel = 1L))
expect_equal(as.numeric(tmp), c(-0.05853477, -0.64056471, -0.48695218))
expect_equal(names(tmp), c("Q2/Q1", "Q3/Q1", "Q4/Q1"))
expect_error(ticQuantileToQuantileLogRatio(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test ticQuantiletoQuantileLogRatio ##
## START unit test numberSpectra ##
test_that("numberSpectra", {
expect_error(numberSpectra(NULL), "unable to find an inherited method")
expect_error(numberSpectra(1:10), "unable to find an inherited method")
expect_equal(numberSpectra(sps_sciex, msLevel = 1L), 1862)
expect_equal(numberSpectra(sps_sciex, msLevel = 2L), 0)
})
## END unit test numberSpectra ##
## START unit test medianPrecursorMz ##
test_that("medianPrecursorMz", {
expect_error(medianPrecursorMz(NULL), "unable to find an inherited method")
expect_error(medianPrecursorMz(1:10), "unable to find an inherited method")
expect_equal(medianPrecursorMz(sps_sciex, msLevel = 1L), 496.4041,
tolerance = 1e-06)
expect_error(medianPrecursorMz(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test medianPrecursorMz ##
## START unit test rtIqr ##
test_that("rtIqr", {
expect_error(rtIqr(NULL), "unable to find an inherited method")
expect_error(rtIqr(1:10), "unable to find an inherited method")
expect_equal(rtIqr(sps_sciex, msLevel = 1L), 129.875)
expect_error(rtIqr(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test rtIqr ##
## START unit test rtIqrRate ##
test_that("rtIqrRate", {
expect_error(rtIqrRate(NULL), "unable to find an inherited method")
expect_error(rtIqrRate(1:10), "unable to find an inherited method")
expect_equal(rtIqrRate(sps_sciex, msLevel = 1L), 7.160731,
tolerance = 1e-06)
expect_error(rtIqrRate(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test rtIqrRate ##
## START unit test areaUnderTic ##
test_that("areaUnderTic", {
expect_error(areaUnderTic(NULL), "unable to find an inherited method")
expect_error(areaUnderTic(1:10), "unable to find an inherited method")
expect_equal(suppressWarnings(areaUnderTic(sps_sciex, msLevel = 1L)),
1273927561)
expect_error(areaUnderTic(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test areaUnderTic ##
## START unit test areaUnderTicRtQuantiles ##
test_that("areaUnderTicRtQuantiles", {
expect_error(areaUnderTicRtQuantiles(NULL), "unable to find an inherited method")
expect_error(areaUnderTicRtQuantiles(1:10), "unable to find an inherited method")
suppressWarnings(tmp <- areaUnderTicRtQuantiles(sps_sciex, msLevel = 1L))
expect_equal(as.numeric(tmp), c(383935723, 368643879, 245834029, 274788917))
expect_equal(names(tmp), c("25%", "50%", "75%", "100%"))
expect_error(areaUnderTicRtQuantiles(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test areaUnderTicRtQuantiles ##
## START unit test extentIdentifiedPrecursorIntensity ##
test_that("extentIdentifiedPrecursorIntensity", {
expect_error(extentIdentifiedPrecursorIntensity(NULL),
"unable to find an inherited method")
expect_error(extentIdentifiedPrecursorIntensity(1:10),
"unable to find an inherited method")
expect_equal(extentIdentifiedPrecursorIntensity(sps_sciex, msLevel = 1L),
1.034276, tolerance = 1e-06)
expect_error(extentIdentifiedPrecursorIntensity(sps_sciex, msLevel = 2),
"'spectra' does not contain any spectra")
})
## END unit test extentIdentifiedPrecursorIntensity ##
## START unit test medianTicRtIqr ##
test_that("medianTicRtIqr", {
expect_error(medianTicRtIqr(NULL), "unable to find an inherited method")
expect_error(medianTicRtIqr(1:10), "unable to find an inherited method")
expect_equal(suppressWarnings(medianTicRtIqr(sps_sciex, msLevel = 1L)),
718615)
expect_error(medianTicRtIqr(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test medianTicRtIqr ##
## START unit test medianTicOfRtRange ##
test_that("medianTicOfRtRange", {
expect_error(medianTicOfRtRange(NULL), "unable to find an inherited method")
expect_error(medianTicOfRtRange(1:10), "unable to find an inherited method")
expect_equal(suppressWarnings(medianTicOfRtRange(sps_sciex, msLevel = 1L)),
804944)
expect_error(medianTicOfRtRange(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test medianTicOfRtRange ##
## START unit test mzAcquisitionRange ##
test_that("mzAcquisitionRange", {
expect_error(mzAcquisitionRange(NULL), "unable to find an inherited method")
expect_error(mzAcquisitionRange(1:10), "unable to find an inherited method")
tmp <- mzAcquisitionRange(sps_sciex, msLevel = 1L)
expect_equal(as.numeric(tmp), c(105, 134), tolerance = 1e-06)
expect_equal(names(tmp), c("min", "max"))
expect_error(mzAcquisitionRange(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test mzAcquisitionRange ##
## START unit test rtAcquisitionRange ##
test_that("rtAcquisitionRange", {
expect_error(rtAcquisitionRange(NULL), "unable to find an inherited method")
expect_error(rtAcquisitionRange(1:10), "unable to find an inherited method")
tmp <- rtAcquisitionRange(sps_sciex, msLevel = 1L)
expect_equal(as.numeric(tmp), c(0.275, 259.757))
expect_equal(names(tmp), c("min", "max"))
expect_error(rtAcquisitionRange(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test rtAcquisitionRange ##
## START unit test precursorIntensityRange ##
test_that("precursorIntensityRange", {
expect_error(precursorIntensityRange(NULL), "unable to find an inherited method")
expect_error(precursorIntensityRange(1:10), "unable to find an inherited method")
tmp <- precursorIntensityRange(sps_sciex, msLevel = 1L)
expect_equal(as.numeric(tmp), c(9679, 10286))
expect_equal(names(tmp), c("min", "max"))
expect_error(precursorIntensityRange(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test precursorIntensityRange ##
## START unit test precursorIntensityQuartiles ##
test_that("precursorIntensityQuartiles", {
expect_error(precursorIntensityQuartiles(NULL), "unable to find an inherited method")
expect_error(precursorIntensityQuartiles(1:10), "unable to find an inherited method")
tmp <- precursorIntensityQuartiles(sps_sciex, msLevel = 1L)
expect_equal(as.numeric(tmp), c(9934, 9999, 10067))
expect_equal(names(tmp), c("25%", "50%", "75%"))
expect_error(precursorIntensityQuartiles(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test precursorIntensityRange ##
## START unit test precursorIntensityMean ##
test_that("precursorIntensityMean", {
expect_error(precursorIntensityMean(NULL), "unable to find an inherited method")
expect_error(precursorIntensityMean(1:10), "unable to find an inherited method")
expect_equal(precursorIntensityMean(sps_sciex, msLevel = 1L), 9999.646,
tolerance = 1e-06)
expect_error(precursorIntensityMean(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test precursorIntensityMean ##
## START unit test precursorIntensitySd ##
test_that("precursorIntensitySd", {
expect_error(precursorIntensitySd(NULL), "unable to find an inherited method")
expect_error(precursorIntensitySd(1:10), "unable to find an inherited method")
expect_equal(precursorIntensitySd(sps_sciex, msLevel = 1L), 101.0341,
tolerance = 1e-06)
expect_error(precursorIntensitySd(sps_sciex, msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test precursorIntensitySd ##
## START unit test msSignal10xChange ##
test_that("msSignal10xChange", {
expect_error(msSignal10xChange(NULL), "unable to find an inherited method")
expect_error(msSignal10xChange(1:10), "unable to find an inherited method")
expect_equal(suppressWarnings(
msSignal10xChange(sps_sciex, change = "jump", msLevel = 1L)), 0)
expect_equal(suppressWarnings(
msSignal10xChange(sps_sciex, change = "fall", msLevel = 1L)), 0)
expect_error(msSignal10xChange(sps_sciex, change = "jump", msLevel = 2L),
"'spectra' does not contain any spectra")
expect_error(msSignal10xChange(sps_sciex, change = "fall", msLevel = 2L),
"'spectra' does not contain any spectra")
})
## END unit test msSignal10xChange ##
## START unit test ratioCharge1over2 ##
test_that("ratioCharge1over2", {
expect_error(ratioCharge1over2(NULL), "unable to find an inherited method")
expect_error(ratioCharge1over2(1:10), "unable to find an inherited method")
expect_equal(ratioCharge1over2(sps_sciex), 0.7 / 0.15, tolerance = 3e-02)
## do not include charges 1 or 2
sps_sciex_foo <- sps_sciex
sps_sciex_foo@backend$precursorCharge <- as.integer(
sample(x = c(1, 2, 3, 4), size = 1862,
replace = TRUE, prob = c(0.0, 0.85, 0.1, 0.05)))
expect_equal(ratioCharge1over2(sps_sciex_foo), NA)
sps_sciex_foo <- sps_sciex
sps_sciex_foo@backend$precursorCharge <- as.integer(
sample(x = c(1, 2, 3, 4), size = 1862,
replace = TRUE, prob = c(0.85, 0.0, 0.1, 0.05)))
expect_equal(ratioCharge1over2(sps_sciex_foo), NA)
})
## END unit test ratioCharge1over2 ##
## START unit test ratioCharge3over2 ##
test_that("ratioCharge3over2", {
expect_error(ratioCharge3over2(NULL), "unable to find an inherited method")
expect_error(ratioCharge3over2(1:10), "unable to find an inherited method")
expect_equal(ratioCharge3over2(sps_sciex), 0.1 / 0.15, tolerance = 2e-02)
## do not include charges 2 or 3
sps_sciex_foo <- sps_sciex
sps_sciex_foo@backend$precursorCharge <- as.integer(
sample(x = c(1, 2, 3, 4), size = 1862,
replace = TRUE, prob = c(0.7, 0.0, 0.25, 0.05)))
expect_equal(ratioCharge3over2(sps_sciex_foo), NA)
sps_sciex_foo <- sps_sciex
sps_sciex_foo@backend$precursorCharge <- as.integer(
sample(x = c(1, 2, 3, 4), size = 1862,
replace = TRUE, prob = c(0.7, 0.25, 0.0, 0.05)))
expect_equal(ratioCharge3over2(sps_sciex_foo), NA)
})
## END unit test ratioCharge3over2 ##
## START unit test ratioCharge4over2 ##
test_that("ratioCharge4over2", {
expect_error(ratioCharge4over2(NULL), "unable to find an inherited method")
expect_error(ratioCharge4over2(1:10), "unable to find an inherited method")
expect_equal(ratioCharge4over2(sps_sciex), 0.05 / 0.15, tolerance = 3e-02)
## do not include charges 2 or 4
sps_sciex_foo <- sps_sciex
sps_sciex_foo@backend$precursorCharge <- as.integer(
sample(x = c(1, 2, 3, 4), size = 1862,
replace = TRUE, prob = c(0.7, 0.0, 0.1, 0.20)))
expect_equal(ratioCharge4over2(sps_sciex_foo), NA)
sps_sciex_foo <- sps_sciex
sps_sciex_foo@backend$precursorCharge <- as.integer(
sample(x = c(1, 2, 3, 4), size = 1862,
replace = TRUE, prob = c(0.7, 0.25, 0.15, 0.0)))
expect_equal(ratioCharge4over2(sps_sciex_foo), NA)
})
## END unit test ratioCharge4over2 ##
test_that(".rtOrderSpectra works", {
tmp <- sps_sciex[sample(seq_along(sps_sciex), 10)]
res <- .rtOrderSpectra(tmp)
expect_true(!is.unsorted(rtime(res)))
tmp$rtime[4] <- NA
expect_warning(res <- .rtOrderSpectra(tmp))
expect_equal(rtime(res), rtime(tmp))
})
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