context("transformIntensity") s <- createMassSpectrum(mass=1:10, intensity=(1:10)^2) test_that("transformIntensity shows warnings", { expect_warning(transformIntensity( createMassSpectrum(mass=double(), intensity=double()), method="sqrt"), "empty") }) test_that("transformIntensity", { expect_equal(intensity(transformIntensity(s, method="sqrt")), 1:10) expect_equal(intensity(transformIntensity(s, method="log")), log((1:10)^2)) expect_equal(intensity(transformIntensity(s, method="log2")), log2((1:10)^2)) expect_equal(intensity(transformIntensity(s, method="log10")), log10((1:10)^2)) }) test_that("transformIntensity works with list of MassSpectrum objects", { expect_error(transformIntensity(list(x=1, y=1)), "no list of MALDIquant::AbstractMassObject objects") expect_error(transformIntensity(list(s, createMassPeaks(1, 1)), "no list of MALDIquant::AbstractMassObject objects")) r <- createMassSpectrum(mass=1:10, intensity=1:10) expect_equal(transformIntensity(list(s, s), method="sqrt"), list(r, r)) }) test_that(".transformIntensity throws errors", { expect_error(.transformIntensity(s), "is missing") }) test_that(".transformIntensity shows warnings", { expect_warning(.transformIntensity(s, fun=function(x)return(-x)), "Negative intensity values are replaced by zeros.") }) test_that(".transformIntensity", { expect_equal(intensity(.transformIntensity(s, sqrt)), 1:10) expect_equal(length(.transformIntensity(s, MALDIquant:::.movingAverage, halfWindowSize=2)), 10) expect_equal(length(.transformIntensity(s, function(x)as.double(filter(x, rep(1, 5)/5, sides=2)))), 6) expect_equal(intensity(suppressWarnings( .transformIntensity(s, fun=function(x)return(-x)))), rep(0, 10)) }) test_that(".transformIntensity works with list of AbstractMassObject objects", { expect_error(.transformIntensity(list(x=1, y=1)), "no list of MALDIquant::AbstractMassObject objects") expect_error(.transformIntensity(list(s, createMassPeaks(1, 1)), "no list of MALDIquant::AbstractMassObject objects")) r <- createMassSpectrum(mass=1:10, intensity=1:10) expect_equal(.transformIntensity(list(s, s), fun=sqrt), list(r, r)) })
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