tests/testthat/test-data.R

In cubar: Codon Usage Bias Analysis

test_that("internal data is loaded correctly", {
    # test human_mt is of class DNAStringSet and has a length of 13
    expect_equal(class(human_mt), "DNAStringSet", ignore_attr = TRUE)
    expect_equal(length(human_mt), 13)

    # test yeast_cds is of class DNAStringSet and has a length of 6600
    expect_equal(class(yeast_cds), "DNAStringSet", ignore_attr = TRUE)
    expect_equal(length(yeast_cds), 6600)

    # test that yeast_half_life is of class data.frame with 3888 rows and 3 columns
    expect_true("data.frame" %in% class(yeast_half_life))
    expect_equal(nrow(yeast_half_life), 3888)

    # test that yeast_exp is of class data.frame with 6685 rows and 3 columns
    # and column names are: gene_id, gene_name, fpkm
    expect_true("data.frame" %in% class(yeast_exp))
    expect_equal(nrow(yeast_exp), 6685)
    expect_equal(colnames(yeast_exp), c("gene_id", "gene_name", "fpkm"))

    # test yeast_cds is of class RNAStringSet and has a length of 275
    expect_equal(class(yeast_trna), "RNAStringSet", ignore_attr = TRUE)
    expect_equal(length(yeast_trna), 275)

    # test that yeast_trna_gcn is a named vector with 41 elements and
    # all names are valid codons
    expect_true(class(yeast_trna_gcn) %in% c("numeric", "integer", "table"))
    expect_equal(length(yeast_trna_gcn), 41)
    expect_true(all(names(yeast_trna_gcn) %in% c(
      "Ala-AGC", "Ala-TGC", "Arg-ACG", "Arg-CCG", "Arg-CCT", "Arg-TCT", "Asn-GTT", "Asp-GTC", "Cys-GCA", "Gln-CTG", "Gln-TTG",
      "Glu-CTC", "Glu-TTC", "Gly-CCC", "Gly-GCC", "Gly-TCC", "His-GTG", "Ile-AAT", "Ile-TAT", "Leu-CAA", "Leu-GAG", "Leu-TAA", 
      "Leu-TAG", "Lys-CTT", "Lys-TTT", "Met-CAT", "Phe-GAA", "Pro-AGG", "Pro-TGG", "Ser-AGA", "Ser-CGA", "Ser-GCT", "Ser-TGA",
      "Thr-AGT", "Thr-CGT", "Thr-TGT", "Trp-CCA", "Tyr-GTA", "Val-AAC", "Val-CAC", "Val-TAC")))

    # test that aa2codon is a data.frame with 64 rows 2 columns: amino_acid, and codon
    # all codons are valid
    # all amino_acids are valid (amino acids are coded like "Ala", "Arg", etc. and stop
    # codons are coded as "*").
    expect_true("data.frame" %in% class(aa2codon))
    expect_equal(nrow(aa2codon), 64)
    expect_equal(ncol(aa2codon), 2)
    expect_true(all(aa2codon$amino_acid %in% c(
        "Ala", "Arg", "Asn", "Asp", "Cys", "Gln", "Glu", "Gly", "His", "Ile",
        "Leu", "Lys", "Met", "Phe", "Pro", "Ser", "Thr", "Trp", "Tyr", "Val", "*")))

})