if (F){
## manual testing
.libPaths(c("~/Toolbox/rlib/",.libPaths()))
library(testthat)
devtools::load_all()
}
# Required for testing
source('tests/testthat/functions/testpaths.R')
func = 'calculate_moderated_ttest'
### testing ###
test_that('Replicates with no normalization',{
id = 'A1'
set.seed(1)
data <- data.frame(gene=LETTERS, rep1 = runif(1:26), rep2=rnorm(1:26))
res = calculate_moderated_ttest(data, normalize = NULL)
ref = testpaths(id, func)$ref
expect_equal_to_reference(res, ref)
#saveRDS(res, paste0('tests/testthat/reference/', func, '/', func, '.', id, '.rds'))
id = 'A2'
set.seed(2)
data <- data.frame(gene=LETTERS, rep1 = runif(1:26), rep2=rnorm(1:26))
res = calculate_moderated_ttest(data, normalize = NULL)
ref = testpaths(id, func)$ref
expect_equal_to_reference(res, ref)
#saveRDS(res, paste0('tests/testthat/reference/', func, '/', func, '.', id, '.rds'))
})
test_that('Triplicates with no normalization',{
id = 'B1'
set.seed(1)
data <- data.frame(gene=LETTERS, rep1 = runif(1:26), rep2=rnorm(1:26), rep3=rnorm(1:26))
res = calculate_moderated_ttest(data, normalize = NULL)
ref = testpaths(id, func)$ref
expect_equal_to_reference(res, ref)
#saveRDS(res, paste0('tests/testthat/reference/', func, '/', func, '.', id, '.rds'))
id = 'B2'
set.seed(2)
data <- data.frame(gene=LETTERS, rep1 = runif(1:26), rep2=rnorm(1:26), rep3=rnorm(1:26))
res = calculate_moderated_ttest(data, normalize = NULL)
ref = testpaths(id, func)$ref
expect_equal_to_reference(res, ref)
#saveRDS(res, paste0('tests/testthat/reference/', func, '/', func, '.', id, '.rds'))
})
test_that('Xplicates',{
## generate data
set.seed(1)
data <- data.frame(gene=LETTERS, rep1 = runif(1:26), rep2=rnorm(1:26), rep3=rnorm(1:26),
rep4=rnorm(1:26), rep5=rnorm(1:26), rep6=rnorm(1:26))
## without normalization
id = 'C1'
res = calculate_moderated_ttest(data, normalize = NULL)
ref = testpaths(id, func)$ref
expect_equal_to_reference(res, ref)
#saveRDS(res, paste0('tests/testthat/reference/', func, '/', func, '.', id, '.rds'))
## With normalization
id = 'C2'
res = calculate_moderated_ttest(data, normalize = 'median')
ref = testpaths(id, func)$ref
expect_equal_to_reference(res, ref)
#saveRDS(res, paste0('tests/testthat/reference/', func, '/', func, '.', id, '.rds'))
})
test_that('Errors are prompted when data format is invalid',{
## this is OK
data <- data.frame(rep1 = runif(1:26), rep2=rnorm(1:26), gene=LETTERS)
res = calculate_moderated_ttest(data)
## 'gene' not in column names
data <- data.frame(rep1 = runif(1:26), rep2=rnorm(1:26), mygene=LETTERS)
expect_error(calculate_moderated_ttest(data))
# replicate not in column name
## this is NOT OK
data <- data.frame(myrname1 = runif(1:26), myrname2=rnorm(1:26), gene=LETTERS)
expect_error(calculate_moderated_ttest(data))
})
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