tests/testthat/test_tpp2dCurveFit.R

In TPP: Analyze thermal proteome profiling (TPP) experiments

dataPath <- system.file("test_data", package="TPP")

# Load function input:
dat2 <- readRDS(file.path(dataPath, "panobinostat_2D_normResults2.rds")) # example input from an older experiment (12 rows)
dat3 <- readRDS(file.path(dataPath, "panobinostat_2D_normResults3.rds")) # example input from an older experiment (20 rows)

# Load expected result for the given input:
out2 <- readRDS(file.path(dataPath, "panobinostat_2D_fitResults2.rds")) # example output from an older experiment (12 rows)
out3 <- readRDS(file.path(dataPath, "panobinostat_2D_fitResults3.rds")) # example output from an older experiment (20 rows)

# test_that("all_ok2", code={
#   skip()
#   datIn <- dat2
#   
#   new <- tpp2dCurveFit(data = datIn, nCores = 1)
#   
#   expect_equal(new, out2)
# })

# test_that("all_ok3", code={
#   skip()
#   datIn <- dat3
#   
#   new <- tpp2dCurveFit(data = datIn, nCores = 1)
#   
#   expect_equal(new %>% mutate(pEC50_quality_check = as.numeric(pEC50_quality_check)), 
#                out3 %>% mutate(pEC50_quality_check = as.numeric(pEC50_quality_check)), 
#                tolerance = 1e-5)
# })

test_that("idCol_updated", code={
  datIn <- dat2
  
  new <- tpp2dCurveFit(data = datIn, nCores = 1)
  
  expect_equal(attr(new, "importSettings")$uniqueIdCol, "Protein_ID")
})

test_that(desc="no_uniqueIdCol", code={
  
  datIn <- dat2
  attr(datIn, "importSettings")$uniqueIdCol <- NULL
  
  expect_error(
    tpp2dCurveFit(data = datIn)
  )
})

test_that(desc="uniqueIdCol_not_character", code={
  
  datIn <- dat2
  attr(datIn, "importSettings")$uniqueIdCol <- numeric()
  
  expect_error(
    tpp2dCurveFit(data = datIn)
  )
})


test_that(desc="uniqueIdCol_not_found", code={
  
  datIn <- dat2
  attr(datIn, "importSettings")$uniqueIdCol <- "nonsense"
  
  expect_error(
    tpp2dCurveFit(data = datIn)
  )
})

test_that(desc="no_nonZeroCols", code={
  
  datIn <- dat2
  attr(datIn, "importSettings")$nonZeroCols <- NULL
  
  expect_error(
    tpp2dCurveFit(data = datIn)
  )
})

test_that(desc="nonZeroCols_not_character", code={
  
  datIn <- dat2
  attr(datIn, "importSettings")$nonZeroCols <- numeric()
  
  expect_error(
    tpp2dCurveFit(data = datIn)
  )
})


test_that(desc="nonZeroCols_not_found", code={
  
  datIn <- dat2
  attr(datIn, "importSettings")$nonZeroCols <- "nonsense"
  
  expect_error(
    tpp2dCurveFit(data = datIn)
  )
})


test_that(desc="warning_deprecated_fct_arg1", code={
  datIn <- dat2
  
  expect_warning(tpp2dCurveFit(data = datIn, configFile = NA))
  
})

test_that(desc="warning_deprecated_fct_arg2", code={
  datIn <- dat2
  
  expect_warning(tpp2dCurveFit(data = datIn, naStrs = NA))
  
})

test_that(desc="warning_deprecated_fct_arg3", code={
  datIn <- dat2
  
  expect_warning(tpp2dCurveFit(data = datIn, fcStr = NA))
  
})

test_that(desc="warning_deprecated_fct_arg4", code={
  datIn <- dat2
  
  expect_warning(tpp2dCurveFit(data = datIn, idVar = NA))
  
})

test_that(desc="warning_deprecated_fct_arg5", code={
  datIn <- dat2
  
  expect_warning(tpp2dCurveFit(data = datIn, nonZeroCols = NA))
  
})

test_that(desc="data_missing", code={
  
  expect_error(
    tpp2dCurveFit()
  )
})