tests/testthat/test-split_multiallelic_snps.R

In prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies

# split_multi_to_biallelic_snps -----------------------------------------------#
test_that("split_multi_to_biallelic_snps() gives expected output when input with only biallelic sites", {

  # Generate biallelic matrix
  test_mat <- matrix(c("A", "T", "G", "C"), nrow = 4, ncol = 5)
  test_mat[1, 1] <- "G"
  test_mat[2, 1] <- "G"
  test_mat[3, 1] <- "A"
  test_mat[4, 1] <- "G"
  colnames(test_mat) <- c("t1", "t2", "t3", "t4", "t5")
  row.names(test_mat) <- c(1, 11, 21, 31)

  test_ar <- matrix(c("A", "T", "G", "C", .9, .8, .7, .4), nrow = 4, ncol = 2)
  colnames(test_ar) <- c("ancestral_allele", "probability")
  row.names(test_ar) <- row.names(test_mat)
  test_ar <- as.data.frame(test_ar)
  test_ar$probability <- as.numeric(as.character(test_ar$probability))

  ref <- c("G", "G", "A", "G")
  alt <- c("A", "T", "G", "C")
  test_split <- split_multi_to_biallelic_snps(mat = test_mat,
                                              ar_results = test_ar,
                                              o_ref = ref,
                                              snpeff = NULL,
                                              o_alt = alt)
  expect_equal(length(test_split), 6)
  expect_true(methods::is(test_split$mat_split, "matrix"))
  expect_true(methods::is(test_split$ar_results_split, "data.frame"))
  expect_true(methods::is(test_split$split_rows_flag, "integer"))
  expect_true(methods::is(test_split$o_ref_split, "character"))
  expect_true(methods::is(test_split$o_alt_split, "character"))
  expect_true(methods::is(test_split$snpeff_split, "NULL"))
  expect_equal(length(test_split$split_rows_flag), nrow(test_split$mat_split))
  expect_equal(test_mat, test_split$mat_split)
})

test_that("split_multi_to_biallelic_snps() gives expected output when input with a quadallelic site", {
  # Generate matrix with one multiallelic line
  test_mat <- matrix(c("A", "T", "G", "C"), nrow = 4, ncol = 5)
  test_mat[1, 1] <- "G"
  test_mat[1, 2] <- "C"
  test_mat[1, 3] <- "T"
  test_mat[2, 1] <- "G"
  test_mat[3, 1] <- "A"
  test_mat[4, 1] <- "G"
  colnames(test_mat) <- c("t1", "t2", "t3", "t4", "t5")
  row.names(test_mat) <- c(1, 11, 21, 31)

  test_ar <- matrix(c("A", "T", "G", "C", .9, .8, .7, .4), nrow = 4, ncol = 2)
  colnames(test_ar) <- c("ancestral_allele", "probability")
  row.names(test_ar) <- row.names(test_mat)
  test_ar <- as.data.frame(test_ar)
  test_ar$probability <- as.numeric(as.character(test_ar$probability))

  ref <- c("G", "G", "A", "G")
  alt <- c("C,T,A", "T", "G", "C")
  test_split <- split_multi_to_biallelic_snps(mat = test_mat,
                                              ar_results = test_ar,
                                              o_ref = ref,
                                              snpeff = NULL,
                                              o_alt = alt)
  expect_equal(length(test_split), 6)
  expect_true(methods::is(test_split$mat_split, "matrix"))
  expect_true(methods::is(test_split$ar_results_split, "data.frame"))
  expect_true(methods::is(test_split$split_rows_flag, "integer"))
  expect_true(methods::is(test_split$o_ref_split, "character"))
  expect_true(methods::is(test_split$o_alt_split, "character"))
  expect_true(methods::is(test_split$snpeff_split, "NULL"))
  expect_equal(length(test_split$split_rows_flag), nrow(test_split$mat_split))
  expect_equal(sum(grepl(1, test_split$split_rows_flag)), 3)
  expect_equal(nrow(test_split$mat_split), nrow(test_mat) + 2)
  expect_equal(test_split$mat_split[1, ], test_split$mat_split[2, ])
  expect_equal(test_split$mat_split[2, ], test_split$mat_split[3, ])
  expect_equal(length(test_split$o_ref_split), 6)
  expect_equal(length(test_split$o_alt_split), 6)

})

test_that("split_multi_to_biallelic_snps() gives error given invalid inputs", {
  expect_error(split_multi_to_biallelic_snps("foo", "bar", "foo", "bar", "foo"))
  expect_error(split_multi_to_biallelic_snps(as.data.frame(matrix(0, 1, 1)),
                                             "bar",
                                             "foo",
                                             "bar",
                                             "foo"))
  expect_error(split_multi_to_biallelic_snps(matrix(0, 1, 1),
                                             "bar",
                                             "foo",
                                             "bar",
                                             "foo"))
})