tests/testthat/test-matchG2A.R

In ASRgenomics: Complementary Genomic Functions

# Get data ----------------------------------------------------------------------------------------------

# Dummy G.
dummymat <-
  matrix(c(1,0,0,0,
           0,1,.25,0,
           0,.25,1,0,
           0, 0, 0, 1),
         byrow = TRUE, nrow = 4,
         dimnames = list(1:4, 1:4))

# Dummy A.
A <- diag(nrow = nrow(dummymat))
A[lower.tri(A)] <- A[upper.tri(A)] <- c(.5,.25,0, 0, 0, 0)
rownames(A) <- colnames(A) <- rownames(dummymat)

# Run tests ---------------------------------------------------------------------------------------------

# Match G2A.
test_that("mathing G2A works", {

  check <- match.G2A(A = A, G = dummymat, clean = TRUE, ord = TRUE, mism = TRUE,
                   RMdiff = TRUE)
  expect_equal(check$Aclean, A)

  # With RM false.
  check <- match.G2A(A = A, G = dummymat, clean = TRUE, ord = TRUE, mism = TRUE,
                   RMdiff = FALSE)
  expect_null(check$RM)

  # With RM false clean false mism FALSE.
  # TODO if matrices dont match and clean is false it just breaks somewhere (maybe add a message here).
  # TODO not sure if the clean argument makes sense. If FALSE and the matrices don't match it will break.
  # TODO if the matrices do match it is not really needed...
  check <- match.G2A(A = A, G = dummymat[1:2, 1:2], clean = TRUE, ord = FALSE, mism = FALSE,
                   RMdiff = FALSE)

  expect_equal(check$Aclean, A[1:2,1:2])

  # With ord false.
  expect_message(
    check <- match.G2A(A = A[3:1, 3:1], G = dummymat, ord = FALSE)
  )

  expect_message(
    check <- match.G2A(A = A[3:1, 3:1], G = dummymat, ord = TRUE)
  )

  # If misgG is produced.
  check <- match.G2A(A = A[1:2, 1:2], G = dummymat, clean = TRUE, ord = FALSE, mism = TRUE,
                   RMdiff = FALSE)
  expect_equal(check$mismG, c("3", "4"))
})

test_that("traps work", {

  # With RM TRUE and CLEAN false.
  expect_error(
    check <- match.G2A(A = A, G = dummymat, clean = FALSE, ord = TRUE, mism = TRUE,
                       RMdiff = TRUE)
  )

  # Wrong classes.
  expect_error(
    check <- match.G2A(A = as.data.frame(A), G = dummymat)
  )

  # Wrong classes.
  expect_error(
    check <- match.G2A(A = A, G = as.data.frame(dummymat))
  )

  # Wrong names.
  Awr <- A
  colnames(Awr) <- NULL

  expect_error(
  check <- match.G2A(A = Awr, G = dummymat)
  )

  Awr <- A
  rownames(Awr) <- NULL

  expect_error(
  check <- match.G2A(A = Awr, G = dummymat)
  )

  dummymatwr <- dummymat
  colnames(dummymatwr) <- NULL

  expect_error(
  check <- match.G2A(A = A, G = dummymatwr)
  )

  dummymatwr <- dummymat
  rownames(dummymatwr) <- NULL

  expect_error(
  check <- match.G2A(A = A, G = dummymatwr)
  )

  dummymatwr <- dummymat
  rownames(dummymatwr) <- 4:1

  expect_error(
  check <- match.G2A(A = A, G = dummymatwr)
  )

  Awr <- A
  rownames(Awr) <- 4:1

  expect_error(
  check <- match.G2A(A = Awr, G = dummymat)
  )
})