tests/testthat/test-dinucleotideFrequencyTest.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

## dinucleotideFrequencyTest exports dinucleotideFrequencyTest()
## for the following classes:
##
## - DNAStringSet
## - RNAStringSet

test_that("examples in dinucleotideFrequencyTest.Rd maintain functionality", {
    ## TODO: better tests.
    ## This is adapted from current functionality, do we know that's correct?
    data(HNF4alpha)
    expect_s3_class(dinucleotideFrequencyTest(HNF4alpha, 1, 2), "htest")

    ## why doesn't p.value have a name?
    test1 <- dinucleotideFrequencyTest(HNF4alpha, 1, 2)
    expect_equal(c(round(test1$statistic,4L),
                   test1$parameter,
                   round(test1$p.value, 4L)),
                 c("X-squared"=19.0727,
                   "df"=9, 0.0246))

    test2 <- dinucleotideFrequencyTest(HNF4alpha, 1, 2, test="G")
    expect_equal(c(round(test2$statistic,4L),
                   test2$parameter,
                   round(test2$p.value,4L)),
                 c("Log likelihood ratio statistic (G)"=17.2609,
                   "X-squared df"=9,
                   "p.value"=0.0448))

    expect_false(grepl("Williams' correction", test2$method))

    test3 <- dinucleotideFrequencyTest(HNF4alpha, 1, 2, test = "adjG")
    expect_equal(c(round(test3$statistic,4L),
                   test3$parameter,
                   round(test3$p.value,4L)),
                 c("Log likelihood ratio statistic (G)"=10.8064,
                   "X-squared df"=9,
                   "p.value"=0.2892))
    expect_true(grepl("Williams' correction", test3$method))
})