tests/testthat/test_abundance.R

In ptm: Analyses of Protein Post-Translational Modifications

library(ptm)
context("Abundance DB")

## ----------------------------------------------- ##
#     Testing the function abundance                #
## ----------------------------------------------- ##
test_that("abundance() works properly", {

  skip_on_cran()
  skip_on_travis()

  a <- abundance(id = 'A0AVT1')
  b <- abundance(id = 'A0AVT1', 'jurkat')
  c <- abundance(id = 'A0AVT1', 'hela')
  d <- abundance(id = 'P30034') # from Sus scrofa
  e <- abundance(id = 'P010091')
  f <- abundance(id = 'G1T1T4') # from Oryctolagus (not present in DB)

  if (!is.null(a)){
    expect_is(a, 'numeric')
    expect_equal(attributes(a)$units, "ppm")
    expect_equal(attributes(a)$species, "Homo sapiens")
    expect_equal(attributes(a)$string, "A0AVT1")
    expect_equivalent(a, 63.7)
  }

  if (!is.null(b)){
    expect_is(b, 'numeric')
    expect_equal(attributes(b)$units, "ppm")
    expect_equal(attributes(b)$species, "Homo sapiens")
    expect_equal(attributes(b)$string, "A0AVT1")
    expect_equivalent(b, 27.4)
  }

  if (!is.null(c)){
    expect_is(c, 'numeric')
    expect_equal(attributes(c)$units, "ppm")
    expect_equal(attributes(c)$species, "Homo sapiens")
    expect_equal(attributes(c)$string, "A0AVT1")
    expect_equivalent(c, 29.3)
  }
  if (!is.null(d)){
    expect_is(d, 'numeric')
    expect_equal(attributes(d)$units, "ppm")
    expect_equal(attributes(d)$species, "Sus scrofa")
    expect_equal(attributes(d)$string, "P30034")
    expect_equivalent(d, 26.9)
  }

  expect_is(e, 'NULL')
  expect_is(f, 'NULL')

})