1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
context("ExperimentList tests")
test_that("ExperimentList constructors work", {
expect_identical(names(ExperimentList()), character())
expect_true(validObject(ExperimentList()))
expect_true(validObject(ExperimentList(list(m=matrix(0, 0, 0)))))
expect_error(ExperimentList(list(matrix(0, 0, 0))),
label="unnamed list element")
m <- matrix(0, 2, 2, dimnames=list(letters[1:2], letters[1:2]))
expect_true(validObject(ExperimentList(list(m=m))))
})
test_that("ExperimentList constructor preserves metadata", {
mcoldf <- DataFrame(AssayNumber=seq_len(length(ExpList)),
row.names = names(ExpList))
mcols(ExpList) <- mcoldf
metalist <- list(Shiny = "Blue Jeans", Old = "Metadata")
metadata(ExpList) <- metalist
nexp <- ExperimentList(ExpList)
expect_identical(mcols(nexp), mcoldf)
expect_identical(metadata(nexp), metalist)
})
test_that("Metadata is kept in ExperimentList when replacing", {
## add metadata columns and metadata
mcoldf <- DataFrame(AssayNumber=seq_len(length(ExpList)),
row.names = names(ExpList))
mcols(ExpList) <- mcoldf
metalist <- list(Shiny = "Blue Jeans", Old = "Metadata")
metadata(ExpList) <- metalist
mae0 <- mae
experiments(mae0) <- ExpList
expect_identical(mcols(experiments(mae0)), mcoldf)
expect_identical(metadata(experiments(mae0)), metalist)
})
test_that("ExperimentList validity function catches non-compatible classes", {
# list
testObj <- list(A = 1:3, B = letters[1:3])
expect_error(ExperimentList(assay1 = testObj))
# List
testObj <- List(A = 1:3, B = letters[1:3])
expect_error(ExperimentList(assay1 = testObj))
testObj <- list(A = matrix(1, 1, dimnames = list("A", "A")))
expect_true(validObject(ExperimentList(assay1 = testObj)))
A <- array(1:24, 4:2, dimnames =
list(letters[1:4], LETTERS[1:3], c("A", "B"))
)
B <- matrix(1:12, ncol=3, dimnames = list(letters[1:4], LETTERS[1:3]))
se2 <- SummarizedExperiment(list(A=A, B=B))
expect_true(validObject(ExperimentList(se2 = se2)))
# top-level DataFrame / data.frame
testObj <- DataFrame(A = 1:3, B = letters[1:3])
testObj1 <- data.frame(A = 1:3, B = letters[1:3])
expect_warning(ExperimentList(assay1 = list(a = testObj)))
expect_warning(ExperimentList(assay1 = list(a = testObj, b = testObj1)))
expect_warning(ExperimentList(assay1 = testObj))
## GRangesList
expect_error(
ExperimentList(list(GR = GRangesList())),
"GRangesList"
)
## vector
expect_error(
ExperimentList(list(int = 1:100L)),
"integer"
)
})
|
