tests/testthat/test-build_formula.R

In Sage-Bionetworks/sageseqr: Identify differentially expressed genes counts data

metadata <- data.frame(
  batch = rep( c("1", "2", "1", "2", "1", "2", "1", "2"), 2),
  diagnosis = rep( c("dx", "dx", "ct", "ct", "dx", "dx", "ct", "ct"), 2),
  sex = rep( c("M", "F", "M", "F", "M", "F", "M", "F"), 2),
  RIN = rep( c(5, 5, 5, 5, 5, 5, 5, 5), 2),
  row.names = c( paste0("S", c(1:16))),
  stringsAsFactors = TRUE
)

output <- build_formula(
  metadata,
  primary_variable = "diagnosis",
  model_variables = "batch"
)

test_that("output data frame subset to primary and model variables.", {
  expect_vector(colnames(output$metadata), c("diagnosis", "batch"))
})

test_that("output is formula.",{
  expect_equal(class(output$formula), "formula")
})

test_that("error if variables are both included and excluded",{
  expect_error(
    build_formula(
      metadata,
      primary_variable = "diagnosis",
      model_variables = "batch",
      exclude_variables = "batch"
      )
    )
})