tests/testthat/test-liftover_coord.R

In RHReynolds/rutils: Common utility functions

context("Testing liftover of genomic coordinates")

# Load data ---------------------------------------------------------------

test_data_path <- system.file("testdata", "liftover_test_data.txt", package = "rutils", mustWork = TRUE)
hg19_path <- system.file("testdata", "hg19ToHg38.over.chain", package = "rutils", mustWork = TRUE)
hg38_path <- system.file("testdata", "hg38ToHg19.over.chain", package = "rutils", mustWork = TRUE)

test_data <-
    readr::read_delim(test_data_path,
        delim = " ",
        col_types =
            readr::cols(
                SNP = readr::col_character(),
                CHR = readr::col_factor(),
                BP_hg19 = readr::col_integer(),
                BP_hg38 = readr::col_integer()
            )
    )


# Testing -----------------------------------------------------------------

test_liftover_hg19 <-
    liftover_coord(
        df = test_data %>%
            dplyr::select(SNP, CHR, BP = BP_hg19),
        path_to_chain = hg19_path
    )

test_liftover_hg38 <-
    liftover_coord(
        df = test_data %>%
            dplyr::select(SNP, CHR, BP = BP_hg38),
        path_to_chain = hg38_path
    )

test_that("liftover_coord correctly converts hg19 to hg38", {
    expect_true(methods::is(test_liftover_hg19, "data.frame"))

    expect_equivalent(
        test_liftover_hg19[["BP"]],
        test_data[["BP_hg38"]]
    )
})

test_that("liftover_coord correctly converts hg38 to hg19", {
    expect_true(methods::is(test_liftover_hg38, "data.frame"))

    expect_equivalent(
        test_liftover_hg38[["BP"]],
        test_data[["BP_hg19"]]
    )
})