expression_data <-
as.data.frame(matrix(1:20, nrow = 5, ncol = 4))
colnames(expression_data) <-
paste0("sample", 1:4)
rownames(expression_data) <-
paste0("variable", 1:5)
sample_info <-
data.frame(
sample_id = colnames(expression_data),
injection.order = 1:4,
class = "QC",
group = "case"
)
variable_info <-
data.frame(
variable_id = rownames(expression_data),
mz = 1:5,
rt = 2:6
)
object <-
create_mass_dataset(
expression_data = expression_data,
sample_info = sample_info,
variable_info = variable_info
)
test_that(desc = "mutate",
code = {
###expression_data
object1 <-
activate_mass_dataset(object, what = "expression_data")
object1 <-
mutate(.data = object1, sample7 = 0)
result1 <-
check_mass_dataset(
expression_data = object1@expression_data,
sample_info = object1@sample_info,
variable_info = object1@variable_info,
sample_info_note = object1@sample_info_note,
variable_info_note = object1@variable_info_note
)
testthat::expect_equal(object = result1, "all good.")
###expression_data2
object1 <-
activate_mass_dataset(object, what = "expression_data")
object1 <-
mutate(.data = object1, sample3 = 0)
result1 <-
check_mass_dataset(
expression_data = object1@expression_data,
sample_info = object1@sample_info,
variable_info = object1@variable_info,
sample_info_note = object1@sample_info_note,
variable_info_note = object1@variable_info_note
)
testthat::expect_equal(object = result1, "all good.")
###sample_info
object2 <-
activate_mass_dataset(object, what = "sample_info")
object2 <-
mutate(.data = object2, group2 = NA)
result2 <-
check_mass_dataset(
expression_data = object2@expression_data,
sample_info = object2@sample_info,
variable_info = object2@variable_info,
sample_info_note = object2@sample_info_note,
variable_info_note = object2@variable_info_note
)
testthat::expect_equal(object = result2, "all good.")
###sample_info2
object2 <-
activate_mass_dataset(object, what = "sample_info")
object2 <-
mutate(.data = object2, group = c("control", rep("case", 3)))
result2 <-
check_mass_dataset(
expression_data = object2@expression_data,
sample_info = object2@sample_info,
variable_info = object2@variable_info,
sample_info_note = object2@sample_info_note,
variable_info_note = object2@variable_info_note
)
testthat::expect_equal(object = result2, "all good.")
###variable_info
object3 <-
activate_mass_dataset(object, what = "variable_info")
object3 <-
mutate(.data = object3, annotation = NA)
result3 <-
check_mass_dataset(
expression_data = object3@expression_data,
sample_info = object3@sample_info,
variable_info = object3@variable_info,
sample_info_note = object3@sample_info_note,
variable_info_note = object3@variable_info_note
)
testthat::expect_equal(object = result3, "all good.")
###variable_info2
object3 <-
activate_mass_dataset(object, what = "variable_info")
object3 <-
mutate(.data = object3, mz = 11:15)
result3 <-
check_mass_dataset(
expression_data = object3@expression_data,
sample_info = object3@sample_info,
variable_info = object3@variable_info,
sample_info_note = object3@sample_info_note,
variable_info_note = object3@variable_info_note
)
testthat::expect_equal(object = result3, "all good.")
})
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