Nothing
context("referencePeaks")
p <- c(createMassPeaks(mass=1:5, intensity=1:5),
createMassPeaks(mass=1:4, intensity=1:4),
createMassPeaks(mass=1:3, intensity=1:3),
createMassPeaks(mass=1:2, intensity=1:2))
p2 <- c(createMassPeaks(mass=c(1, 1.001, 3), intensity=c(2, 1, 1)),
createMassPeaks(mass=c(0.99, 3), intensity=rep(1, 2)),
createMassPeaks(mass=c(1.02, 3), intensity=rep(1, 2)))
test_that("referencePeaks throws errors", {
expect_error(referencePeaks(list(a="a", b="b"), minFrequency=0.5),
"no list of MALDIquant::MassPeaks objects")
expect_error(referencePeaks(p[[1]], minFrequency=0.5),
"no list of MALDIquant::MassPeaks objects")
})
test_that("referencePeaks shows warnings", {
expect_warning(referencePeaks(p, minFrequency=-1),
" < 0 does not make sense! Using 0 instead")
expect_warning(referencePeaks(p, minFrequency=10),
"Empty peak whitelist for level")
})
test_that("referencePeaks works with different frequencies", {
expect_equal(referencePeaks(p, minFrequency=1),
createMassPeaks(mass=1:2, intensity=rep(1, 2)))
expect_equal(referencePeaks(p, minFrequency=0.5),
createMassPeaks(mass=1:4, intensity=c(1, 1, 3/4, 0.5)))
})
test_that("referencePeaks works with different methods", {
expect_equal(referencePeaks(p2, minFrequency=1, tolerance=0.05),
createMassPeaks(mass=3, intensity=1))
expect_equal(referencePeaks(p2, method="strict", minFrequency=1,
tolerance=0.05),
createMassPeaks(mass=3, intensity=1))
expect_equal(referencePeaks(p2, method="relaxed", minFrequency=1,
tolerance=0.05),
createMassPeaks(mass=c(1+1/300, 3), intensity=rep(1, 2)))
})
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