Nothing
context("binPeaks")
p <- list(createMassPeaks(mass=seq(100, 500, 100), intensity=1:5),
createMassPeaks(mass=c(seq(100.2, 300.2, 100), 395), intensity=1:4))
p2 <- c(createMassPeaks(mass=c(1.009, 1.01, 3), intensity=c(2, 1, 1), snr=1:3),
createMassPeaks(mass=c(1, 3), intensity=1:2, snr=1:2),
createMassPeaks(mass=c(1.03, 3), intensity=1:2, snr=1:2))
test_that("binPeaks throws errors", {
expect_error(binPeaks(list()), "no list of MALDIquant::MassPeaks")
expect_error(binPeaks(p, method="foobar"),
".*arg.* should be one of .*strict.*, .*relaxed.*")
})
test_that("binPeaks bins peaks strict", {
b <- binPeaks(p, tolerance=0.002)
expect_true(all(b[[1]]@mass[1:3]==b[[2]]@mass[1:3]))
expect_false(all(b[[1]]@mass[4]==b[[2]]@mass[4]))
expect_true(length(b[[1]])==5)
expect_true(length(b[[2]])==4)
expect_false(all(p[[1]]@mass==b[[1]]@mass))
expect_false(all(p[[2]]@mass==b[[2]]@mass))
b <- binPeaks(p, tolerance=0.1)
expect_true(all(b[[1]]@mass[1:4]==b[[2]]@mass[1:4]))
expect_true(length(b[[1]])==5)
expect_true(length(b[[2]])==4)
expect_false(all(p[[1]]@mass==b[[1]]@mass))
expect_false(all(p[[2]]@mass==b[[2]]@mass))
})
test_that("binPeaks bins peaks releaxed", {
b <- binPeaks(p2, method="relaxed", tolerance=0.05)
expect_true(all(b[[1]]@mass==c(1.01, 1.013, 3)))
ip <- sort(p2[[1]]@mass, index.return=TRUE)
ib <- sort(b[[1]]@mass, index.return=TRUE)
expect_equal(ip$ix, ib$ix)
expect_false(all(p2[[1]]@intensity == b[[1]]@intensity))
expect_false(all(p2[[1]]@snr== b[[1]]@snr))
expect_true(all(b[[1]]@intensity == c(1, 2, 1)))
expect_true(all(b[[2]]@intensity == 1:2))
expect_true(all(b[[3]]@intensity == 1:2))
expect_true(all(b[[1]]@snr == c(2, 1, 3)))
expect_true(all(b[[2]]@snr == 1:2))
expect_true(all(b[[3]]@snr == 1:2))
})
test_that("binPeaks bins peaks to reference", {
ref <- createMassPeaks(mass=1:3, intensity=1:3, snr=1:3)
r <- c(createMassPeaks(mass=c(1, 1.01, 3), intensity=c(2, 1, 1), snr=1:3),
createMassPeaks(mass=c(1, 3), intensity=1:2, snr=1:2),
createMassPeaks(mass=c(1, 3), intensity=1:2, snr=1:2))
expect_equal(binPeaks(c(ref, p2), method="reference", tolerance=0.05)[-1], r)
})
test_that("binPeaks don't introduce new peaks; issue 61", {
p1 <- createMassPeaks(1:5, 1:5, metaData=list(name="foo"))
p0 <- createMassPeaks(numeric(), numeric(), metaData=list(name="bar"))
expect_equal(binPeaks(list(p1, p0)), list(p1, p0))
expect_equal(binPeaks(list(p0, p1)), list(p0, p1))
expect_equal(binPeaks(list(p0, p0, p1)), list(p0, p0, p1))
expect_equal(binPeaks(list(p0, p1, p1)), list(p0, p1, p1))
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.