tests/testthat/test_getGenotypes.R

In nprcgenekeepr: Genetic Tools for Colony Management

#' Copyright(c) 2017-2024 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("getGenotypes")
## This is identical to getPedigree and needs to be strengthened. However,
## function does not do any data quality checks at this time.

test_that("getGenotypes recognizes no file and wrong file arguments", {
  expect_error(getGenotypes(), "\"fileName\" is missing, with no default")
})
test_that("getGenotypes recognizes and opens Excel files.", {
  pedExcel <-
    suppressWarnings(getGenotypes(
      fileName = system.file("testdata", "qcPed.xlsx",
        package =
          "nprcgenekeepr"
      )
    ))
  expect_identical(nrow(pedExcel), 280L)
})
test_that(
  paste0(
    "getGenotypes recognizes and opens CSV files with default ",
    "comma separator."
  ),
  {
    pedCsv <-
      getGenotypes(fileName = system.file("testdata", "qcPed.csv",
        package =
          "nprcgenekeepr"
      ))
    expect_identical(nrow(pedCsv), 280L)
  }
)
test_that(
  paste0(
    "getGenotypes recognizes and opens CSV files with specified ",
    "comma separator."
  ),
  {
    pedCsv2 <-
      getGenotypes(
        fileName = system.file("testdata", "qcPed.csv",
          package =
            "nprcgenekeepr"
        ),
        sep = ","
      )
    expect_identical(nrow(pedCsv2), 280L)
  }
)
test_that(
  paste0(
    "getGenotypes recognizes and opens .txt files with specified ",
    "tab separator."
  ),
  {
    pedTxt <-
      getGenotypes(
        fileName = system.file("testdata", "qcPed.txt",
          package =
            "nprcgenekeepr"
        ),
        sep = "\t"
      )
    expect_identical(nrow(pedTxt), 280L)
  }
)