tests/testthat/test_MVAobjects.R

In kimsche/MetaboMate: All you need for NMR-based metabolic profiling with R!

context("Panoptikum: read bruker, dummy var, MVA objects")

path=system.file("extdata/", package = "MetaboMate")
readBruker(path)


#qcs=spec.quality(X, ppm, ppm.noise=c(14,14.1), plot=F)
#qcs_e1=evaluate_promise(spec.quality(X, ppm[-1], ppm.noise=c(14,14.1), plot=F))



test_that('read-in Bruker files', {
  expect_equal(length(which(is.na(X))), 0)
  expect_equal(length(which(is.na(ppm))), 0)
  expect_equal(nrow(X), 30)
  expect_equal(nrow(meta), 30)
  expect_equal(length(ppm), ncol(X))
})

#### read bruker
test_that('spec quality', {
  qcs=spec.quality(X, ppm, ppm.noise=c(14,14.1), plot=F)
  expect_equal(nrow(qcs), 30)
  expect_equal(length(which(is.na(qcs))), 0)
  expect_error(spec.quality(X, ppm[-1], ppm.noise=c(14,14.1), plot=F),'Ppm vector does not match to NMR matrix dimension.', fixed=T)
  expect_error(spec.quality(X, ppm, ppm.noise=c(94,94.1), plot=F), 'Chemical shift specified in ppm.noise variable is not included in ppm vector (out of range).', fixed=T)



})

#### dummy var
Y=factor(rep(LETTERS[1:3], each=5))
out=MetaboMate:::create_dummy_Y(Y)[[1]]

test_that('output dummy var from vector', {
  expect_equal(ncol(out), 3)
  expect_equal(length(unique(out[,1])), 2)
  expect_equal(length(unique(out[,2])), 2)
  expect_equal(length(unique(out[,3])), 2)
})

#### S4 slots
s <- new("PCA_MetaboMate")
test_that('Number of slots in PCA object', {
  expect_equal(length(slotNames(s)), 5)
})

s <- new("OPLS_MetaboMate")
test_that('Number of slots in OPLS object', {
  expect_equal(length(slotNames(s)), 22)
})