test_that("data loads correctly", {
example_files <- list.files(system.file('extdata', package = 'MetaboTandem'),
pattern = 'test.mzML', full.names = TRUE)
metadata <- data.frame(FileName = example_files,
SampleID = c('RP_1_test', 'RP_2_test'),
treatment = 1)
rp_data <- load_spectra_data(system.file('extdata', package = 'MetaboTandem'),
metadata = metadata,
format = 'mzML')
expect_true(is(rp_data, 'OnDiskMSnExp'))
})
test_that('data is transformed to centroided correctly', {
data("rp_data", package = 'MetaboTandem')
data_cent <- centroid_check(rp_data, transform = TRUE)
is.centroided <- unique(MSnbase::fData(data_cent)$centroided)
expect_true(is.centroided)
})
test_that('peaks can be picked', {
data("rp_data", package = 'MetaboTandem')
data_cent <- centroid_check(rp_data, transform = TRUE)
data_cent <- apply_peak_picking(data_cent,
p.width = c(20, 50),
snt = 0,
noise = 10000)
expect_true(xcms::hasChromPeaks(data_cent))
})
test_that('alignment and correspondence work', {
data("rp_data", package = 'MetaboTandem')
data_cent <- centroid_check(rp_data, transform = TRUE)
data_cent <- apply_peak_picking(data_cent,
p.width = c(20, 50),
snt = 0,
noise = 1000)
data_align <- apply_alignment(data = data_cent,
metadata = MSnbase::pData(data_cent),
min_frac = 0.5,
min_samples = 1,
group_by = 'treatment',
plot = FALSE)
data_grouped <- apply_correspondence(data_align,
metadata = MSnbase::pData(data_cent),
min_frac = 0.5,
min_samples = 1,
group_by = 'treatment')
expect_true(xcms::hasAdjustedRtime(data_align))
expect_true(xcms::hasFeatures(data_grouped))
})
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