tests/testthat/test_checkGenotypeFile.R

In nprcgenekeepr: Genetic Tools for Colony Management

#' Copyright(c) 2017-2024 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("checkGenotypeFile")
library(stringi) # nolint undesirable_function_linter.

ped <- nprcgenekeepr::qcPed
ped <- ped[order(ped$id), ]
genotype <- data.frame(
  id = ped$id[50L + 1L:20L],
  first_name = stri_c("first_name", 1L:20L),
  second_name = stri_c("second_name", 1L:20L),
  stringsAsFactors = FALSE
)

test_that("checkGenotypeFile allows correct dataframe", {
  expect_error(checkGenotypeFile(genotype), NA)
})
test_that("checkGenotypeFile disallows dataframe with < 3 columns", {
  expect_error(
    checkGenotypeFile(genotype[, c("id", "first_name")]),
    "Genotype file must have at least three columns."
  )
})
test_that("checkGenotypeFile ensures 'id' as the first column.", {
  names(genotype) <- c("ego", "first_name", "second_name")
  expect_error(
    checkGenotypeFile(genotype),
    "Genotype file must have 'id' as the first column."
  )
})
test_that(paste0(
  "checkGenotypeFile ensures cannot have a column named ",
  "'first' or 'second'."
), {
  names(genotype) <- c("id", "first", "second_name")
  expect_error(
    checkGenotypeFile(genotype),
    "Genotype file cannot have a column named 'first' or 'second'."
  )
})
genotype <- data.frame(
  id = ped$id[50L + 1L:20L],
  first_name = stri_c("first_name", 1L:20L),
  second_name = stri_c("sec:ond_name", 1L:20L),
  stringsAsFactors = FALSE
)
test_that("checkGenotypeFile detects a bad dataframe", {
  expect_true(inherits(checkGenotypeFile(genotype), "data.frame"))
})
genotype <- data.frame(
  id = ped$id[50L + 1L:20L],
  first_name = stri_c("first_name", 1L:20L),
  second_name = stri_c("second_name", 1L:20L),
  stringsAsFactors = FALSE
)
genotype$first_name[genotype$id == "1X1237"] <- "almost; ok"
test_that("checkGenotypeFile detects single error", {
  expect_s3_class(checkGenotypeFile(genotype), "data.frame")
})
genotype <- data.frame(
  id = ped$id[50L + 1L:20L],
  first_name = stri_c("first_name", 1L:20L),
  second = stri_c("second_name", 1L:20L),
  stringsAsFactors = FALSE
)
test_that("checkGenotypeFile detects illegal column name", {
  expect_error(checkGenotypeFile(genotype))
})
genotype <- data.frame(
  id = ped$id[50L + 1L:20L],
  first_name = stri_c(10001L:10020L),
  second_name = stri_c("second_name", 1L:20L),
  stringsAsFactors = FALSE
)
test_that(stri_c(
  "checkGenotypeFile checks for ossible collision on allele(s) ",
  "interpreted as a number"
), {
  expect_error(checkGenotypeFile(genotype))
})