Nothing
context("estimateBaseline")
s <- createMassSpectrum(mass=1:20, intensity=rep(10:1, 2))
test_that("estimateBaseline throws errors", {
expect_error(estimateBaseline(s, method="foobar"),
".*arg.* should be one of .*SNIP.*, .*ConvexHull.*, .*median.*")
})
test_that("estimateBaseline shows warnings", {
expect_warning(estimateBaseline(
createMassSpectrum(mass=double(), intensity=double()),
"empty"))
})
test_that("estimateBaselineConvexHull", {
b <- c(10:1, rep(1, 10))
m <- cbind(mass=mass(s), intensity=b)
expect_identical(MALDIquant:::.estimateBaselineConvexHull(mass(s),
intensity(s)), b)
## user method
expect_identical(estimateBaseline(s, method="ConvexHull"), m)
})
test_that("estimateBaselineMedian", {
b <- c(10:4, rep(c(3, 8), each=3), 7:1)
b1 <- c(10:3, rep(c(2, 9), each=2), 8:1)
m <- cbind(mass=mass(s), intensity=b)
expect_identical(MALDIquant:::.estimateBaselineMedian(mass(s), intensity(s),
1), b1)
expect_identical(MALDIquant:::.estimateBaselineMedian(mass(s), intensity(s),
2), b)
## user method
expect_identical(estimateBaseline(s, method="median", halfWindowSize=2), m)
## halfWindowSize
expect_error(MALDIquant:::.estimateBaselineMedian(mass(s), intensity(s), 0),
"too small")
expect_error(MALDIquant:::.estimateBaselineMedian(mass(s), intensity(s), 20),
"too large")
})
test_that("estimateBaselineSnip", {
b <- list(decreasing=list(b=c(10:1, c(2.5, 4.0, 5.5), 7:1),
b100=c(10:1, rep(c(1.25, 1.5, 1.75, 1.375, 1),
times=2))),
increasing=list(b=c(10:1, 5:4, 5.5, 7:1),
b100=c(10:1, 3.75, 3.375, 3:1, 2.5, 4:1)))
## test default decreasing argument
expect_identical(MALDIquant:::.estimateBaselineSnip(mass(s), intensity(s), 2),
b$decreasing$b)
for (j in seq(along=b)) {
d <- names(b)[j] == "decreasing"
expect_identical(MALDIquant:::.estimateBaselineSnip(mass(s), intensity(s),
2, decreasing=d),
b[[j]]$b)
expect_equal(MALDIquant:::.estimateBaselineSnip(mass(s), intensity(s),
decreasing=d),
b[[j]]$b100)
## user method
m <- cbind(mass=mass(s), intensity=b[[j]]$b)
m100 <- cbind(mass=mass(s), intensity=b[[j]]$b100)
expect_identical(estimateBaseline(s, method="SNIP", iterations=2,
decreasing=d), m)
expect_identical(estimateBaseline(s, iterations=2, decreasing=d), m)
expect_equal(estimateBaseline(s, decreasing=d), m100)
}
})
test_that("estimateBaselineTopHat", {
b <- c(rep(8, 3), 7:1, rep(6, 5), 5:1)
b1 <- c(rep(9, 2), 8:1, rep(8, 3), 7:1)
m <- cbind(mass=mass(s), intensity=b)
expect_identical(MALDIquant:::.estimateBaselineTopHat(mass(s), intensity(s),
1), b1)
expect_identical(MALDIquant:::.estimateBaselineTopHat(mass(s), intensity(s),
2), b)
## user method
expect_identical(estimateBaseline(s, method="TopHat", halfWindowSize=2), m)
## halfWindowSize
expect_error(MALDIquant:::.estimateBaselineTopHat(mass(s), intensity(s), 0),
"too small")
expect_error(MALDIquant:::.estimateBaselineTopHat(mass(s), intensity(s), 20),
"too large")
})
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