tests/testthat/test_utils.R

In ComputationalProteomicsUnit/Pbase: Manipulating and exploring protein and proteomics data

context("utils")

test_that(".addColumn", {
    d <- data.frame(a = 1:3, b = 4:6)
    result <- data.frame(a = 1:3, b = 4:6, c = 7:9)
    resultForced <- data.frame(a = 1:3, b = 7:9)

    expect_error(Pbase:::.addColumn(list()))
    expect_error(Pbase:::.addColumn(d))
    expect_error(Pbase:::.addColumn(d, character()))
    expect_error(Pbase:::.addColumn(d, ""))
    expect_error(Pbase:::.addColumn(d, "b", integer()))
    expect_error(Pbase:::.addColumn(d, "b", 7:9),
                 "The column .*b.* already exists.")

    expect_equal(Pbase:::.addColumn(d, "c", 7:9), result)
    expect_equal(Pbase:::.addColumn(d, "b", 7:9, force = TRUE), resultForced)
})

test_that(".isInRange", {
    x <- 1:10
    result <- rep(c(FALSE, TRUE, FALSE), c(2, 4, 4))
    expect_error(Pbase:::.isInRange(x, 3))
    expect_error(Pbase:::.isInRange(x, "foo"))
    expect_equal(Pbase:::.isInRange(x, c(3, 6)), result)
    expect_equal(Pbase:::.isInRange(x, c(6, 3)), result)
    expect_equal(Pbase:::.isInRange(x, c(1, 20)), rep(TRUE, 10))
    expect_equal(Pbase:::.isInRange(x, c(11, 20)), rep(FALSE, 10))
})

test_that(".flatIRangesList", {
    expect_error(Pbase:::.flatIRangesList(list()))

    irl <- IRangesList(IRanges(start = c(1, 5), end = c(3, 10)),
                       IRanges(start = c(7, 10), end = c(9, 15)))
    result <- IRanges(start = c(1, 5, 7, 10), end = c(3, 10, 9, 15))
    resultShift <- IRanges(start = c(1, 5, 17, 20), end = c(3, 10, 19, 25))
    resultShiftBy <- IRanges(start = c(2, 6, 27, 30), end = c(4, 11, 29, 35))

    expect_equal(Pbase:::.flatIRangesList(irl), result)
    expect_equal(Pbase:::.flatIRangesList(irl, shift = TRUE), resultShift)
    expect_equal(Pbase:::.flatIRangesList(irl, shift = TRUE,
                                          shiftBy = c(1, 20)), resultShiftBy)

})

test_that(".setNames2", {
    x <- 1:3
    nm1 <- LETTERS[1:3]
    nm2 <- setNames(LETTERS[1:3], LETTERS[4:6])
    expect_equal(Pbase:::.setNames2(x, nm1), setNames(x, nm1))
    expect_equal(Pbase:::.setNames2(x, nm2), setNames(x, names(nm2)))
})

test_that(".singleAA", {
    x1 <- "ABC"
    x2 <- c(a = "ABC", b = "DEF")
    x3 <- AAString(x1)
    x4 <- AAStringSet(x2)
    x5 <- AAStringSetList(list(P1=x2, P2=x2[2]))
    result1 <- list(LETTERS[1:3])
    result2 <- list(a = LETTERS[1:3], b = LETTERS[4:6])
    result5 <- list(P1=LETTERS[1:3], P1=LETTERS[4:6], P2=LETTERS[4:6])
    expect_equal(Pbase:::.singleAA(x1), result1)
    expect_equal(Pbase:::.singleAA(x2), result2)
    expect_equal(Pbase:::.singleAA(x3), result1)
    expect_equal(Pbase:::.singleAA(x4), result2)
    expect_equal(Pbase:::.singleAA(x5), result5)
})

test_that(".singular", {
    x1 <- c(1, 2, 2, 3, 1, 5, 4, 3, 2, 1)
    x2 <- rep(1, 10)
    x3 <- 1:5
    expect_equal(Pbase:::.singular(x1), c(5, 4))
    expect_equal(Pbase:::.singular(x2), double())
    expect_equal(Pbase:::.singular(x3), 1:5)
})

test_that(".checkPcol", {
    ep <- new("Proteins")
    expect_error(Pbase:::.checkPcol(ep, "any"))
    ## Get a Proteins object from the database.
    library(EnsDb.Hsapiens.v86)
    library(ensembldb)
    edb <- EnsDb.Hsapiens.v86
    p_2 <- Proteins(edb, filter = TxIdFilter("ENST00000335953"))
    ## Check we gete ProteinDomains back
    pc <- Pbase:::.checkPcol(p_2)
    expect_equal(pc, "ProteinDomains")
    pc <- Pbase:::.checkPcol(p_2, "ProteinDomains")
    expect_equal(pc, "ProteinDomains")
    ## Check exception
    expect_error(Pbase:::.checkPcol(p_2, "other"))
})