tests/testthat/test-method.approx.R

In aravind-j/rmelting: R Interface to MELTING 5

context("Approximative methods are OK")

test_that("tests for method.approx - DNA/DNA", {
  DNAseq <- c("TCTAATGTGCTGTTAGATGTATCCAGAGATAGCCGAGCATAAACTTCAACACACGAGACGTTGATTGGATTTAACCATAG")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna",
                       Na.conc = 1)$Results$`Melting temperature (C)`,
               87.82455, tolerance = 1e-5, label = "DNA/DNA default")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna", Na.conc = 1,
                       method.approx = "wetdna91")$Results$`Melting temperature (C)`,
               87.82455, tolerance = 1e-5, label = "wetdna91")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna", Na.conc = 1,
                       method.approx = "ahs01")$Results$`Melting temperature (C)`,
               87.325, tolerance = 1e-5, label = "ahs01")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna", Na.conc = 1,
                       method.approx = "che93")$Results$`Melting temperature (C)`,
               77.575, tolerance = 1e-5, label = "che93")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna", Na.conc = 1,
                       method.approx = "che93corr")$Results$`Melting temperature (C)`,
               79.0125, tolerance = 1e-5, label = "che93corr")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna", Na.conc = 1,
                       method.approx = "schdot")$Results$`Melting temperature (C)`,
               89.4625, tolerance = 1e-5, label = "schdot")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna", Na.conc = 1,
                       method.approx = "owe69")$Results$`Melting temperature (C)`,
               100.96, tolerance = 1e-5, label = "owe69")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnadna", Na.conc = 1,
                       method.approx = "san98")$Results$`Melting temperature (C)`,
               86.9, tolerance = 1e-5, label = "san98")
})

test_that("tests for method.approx - RNA/RNA", {
  RNAseq <- c("UUAAUCUCCGUCAUCUUUAAGCCGUGGAGAGACUGUAGACUUGAACAGGGGUAAGCGGAGGCACGUAGGAUUCACAUCAU")

  expect_equal(melting(sequence = RNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "rnarna",
                       Na.conc = 1)$Results$`Melting temperature (C)`,
               101.1745, tolerance = 1e-5, label = "RNA/RNA default")

  expect_equal(melting(sequence = RNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "rnarna", Na.conc = 1,
                       method.approx = "wetrna91")$Results$`Melting temperature (C)`,
               101.1745, tolerance = 1e-5, label = "wetrna91")
})

test_that("tests for method.approx - DNA/RNA", {
  DNAseq <- c("TCTAATGTGCTGTTAGATGTATCCAGAGATAGCCGAGCATAAACTTCAACACACGAGACGTTGATTGGATTTAACCATAG")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnarna",
                       Na.conc = 1)$Results$`Melting temperature (C)`,
               88.92455, tolerance = 1e-5, label = "DNA/RNA default")

  expect_equal(melting(sequence = DNAseq, nucleic.acid.conc = 2e-06,
                       hybridisation.type = "dnarna", Na.conc = 1,
                       method.approx = "wetdnarna91")$Results$`Melting temperature (C)`,
               88.92455, tolerance = 1e-5, label = "wetdnarna91")
})