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test_that("test_Accessor", {
pfm <- PFMatrix(ID = "MA0004.1", name = "Arnt", matrixClass = "Zipper-Type",
strand = "+", bg = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
tags = list(family = "Helix-Loop-Helix", species = "10090",
tax_group = "vertebrates", medline = "7592839", type = "SELEX",
ACC = "P53762", pazar_tf_id = "TF0000003", TFBSshape_ID = "11",
TFencyclopedia_ID = "580"), profileMatrix = matrix(c(4L,
19L, 0L, 0L, 0L, 0L, 16L, 0L, 20L, 0L, 0L, 0L, 0L,
1L, 0L, 20L, 0L, 20L, 0L, 0L, 0L, 0L, 20L, 0L), byrow = TRUE,
nrow = 4, dimnames = list(c("A", "C", "G", "T"))))
expect_identical("MA0004.1", ID(pfm))
expect_identical("Arnt", name(pfm))
expect_identical("Zipper-Type", matrixClass(pfm))
})
test_that("test_XMatrixConstructor", {
expect_error(PFMatrix(pseudocounts = 0.8))
expect_error(PWMatrix(schneider = TRUE))
expect_error(PFMatrix(bg = c(A = 0.25, C = 0.25, G = 0.25,
U = 0.25)))
expect_error(PFMatrix(bg = c(A = -0.5, C = 0.25, G = 0.25,
T = 0.25)))
expect_error(PFMatrix(bg = c(A = -0.5, C = 0.25, T = 0.25,
G = 0.25)))
expect_error(PFMatrix(ID = c("12", "34")))
expect_error(PFMatrix(name = c("12", "34")))
expect_error(PFMatrix(strand = c("+", "-")))
expect_error(PFMatrix(strand = c("a")))
expect_error(PFMatrix(profileMatrix = matrix(1, ncol = 2,
nrow = 2)))
})
test_that("test_XMatrixListConstructor", {
expect_error(PFMatrixList(PWMatrix(), PWMatrix()))
expect_error(PWMatrixList(PFMatrix(), PFMatrix()))
expect_error(ICMatrixList(PWMatrix(), PWMatrix()))
})
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