tests/testthat/test_checkGenotypeFile.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Copyright(c) 2017-2020 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("checkGenotypeFile")
library(testthat)
library(stringi)

ped <- nprcgenekeepr::qcPed
ped <- ped[order(ped$id), ]
genotype <- data.frame(id = ped$id[50 + 1:20],
                       first_name = stri_c("first_name", 1:20),
                       second_name = stri_c("second_name", 1:20),
                       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$id[50 + 1:20],
                       first_name = stri_c("first_name", 1:20),
                       second_name = stri_c("sec:ond_name", 1:20),
                       stringsAsFactors = FALSE)
test_that("checkGenotypeFile detects a bad dataframe", {
  expect_true(is.data.frame(checkGenotypeFile(genotype)))
})
genotype <- data.frame(id = ped$id[50 + 1:20],
                       first_name = stri_c("first_name", 1:20),
                       second_name = stri_c("second_name", 1:20),
                       stringsAsFactors = FALSE)
genotype$first_name[genotype$id == "1X1237"] <- "almost; ok"
test_that("checkGenotypeFile detects single error", {
  expect_true(is.data.frame(checkGenotypeFile(genotype)))
})
genotype <- data.frame(id = ped$id[50 + 1:20],
                       first_name = stri_c("first_name", 1:20),
                       second = stri_c("second_name", 1:20),
                       stringsAsFactors = FALSE)
test_that("checkGenotypeFile detects illegal column name", {
  expect_error(checkGenotypeFile(genotype))
})
genotype <- data.frame(id = ped$id[50 + 1:20],
                       first_name = stri_c(10001:10020),
                       second_name = stri_c("second_name", 1:20),
                       stringsAsFactors = FALSE)
test_that(stri_c("checkGenotypeFile checks for ossible collision on allele(s) ",
                 "interpreted as a number"), {
  expect_error(checkGenotypeFile(genotype))
})