... | ... |
@@ -1,6 +1,6 @@ |
1 | 1 |
Package: dcanr |
2 | 2 |
Title: Differential co-expression/association network analysis |
3 |
-Version: 0.99.2 |
|
3 |
+Version: 0.99.3 |
|
4 | 4 |
Authors@R: person("Dharmesh", "Bhuva", email = "bhuva.d@wehi.edu.au", role = c("aut", "cre"), comment = c(ORCID = '0000-0002-6398-9157')) |
5 | 5 |
Description: Methods and an evaluation framework for the inference of differential co-expression/association networks. |
6 | 6 |
biocViews: NetworkInference, GraphAndNetwork, DifferentialExpression, Network |
... | ... |
@@ -13,19 +13,29 @@ colnames(x) = 1:ncol(x) |
13 | 13 |
rownames(x) = 1:nrow(x) |
14 | 14 |
cond <- rep(1:2, each = 30) |
15 | 15 |
|
16 |
+#define methods |
|
17 |
+infmethods = dcMethods() |
|
18 |
+if (!require('EBcoexpress')) { |
|
19 |
+ infmethods = setdiff(infmethods, 'ebcoexpress') |
|
20 |
+} |
|
21 |
+if (!require('COSINE')) { |
|
22 |
+ infmethods = setdiff(infmethods, 'ecf') |
|
23 |
+} |
|
24 |
+ |
|
16 | 25 |
test_that('Inference method calls work', { |
17 | 26 |
expect_is(dcScore(x, cond), 'matrix') |
18 | 27 |
expect_is(dcScore(x, cond, dc.method = 'zscore'), 'matrix') |
19 |
- for (m in setdiff(dcMethods(), 'ebcoexpress')) { |
|
28 |
+ for (m in infmethods) { |
|
20 | 29 |
expect_is(dcScore(x, cond, !!m), 'matrix') |
21 | 30 |
} |
22 | 31 |
|
23 | 32 |
try(detach('package:EBcoexpress', unload = T), silent = TRUE) |
24 | 33 |
try(detach('package:mclust', unload = T), silent = TRUE) |
25 | 34 |
try(detach('package:minqa', unload = T), silent = TRUE) |
26 |
- expect_error(dcScore(x, cond, 'ebcoexpress'), 'loading the EBcoexpress library') |
|
27 |
- library(EBcoexpress) |
|
28 |
- expect_is(dcScore(x, cond, 'ebcoexpress'), 'matrix') |
|
35 |
+ if(require(EBcoexpress)) |
|
36 |
+ expect_is(dcScore(x, cond, 'ebcoexpress'), 'matrix') |
|
37 |
+ else |
|
38 |
+ expect_error(dcScore(x, cond, 'ebcoexpress'), '\'EBcoexpress\' needed for this function to work') |
|
29 | 39 |
|
30 | 40 |
expect_error(dcScore(x, cond, 'fakemethod'), 'not TRUE') |
31 | 41 |
expect_error(dcScore(x, cond, cor.method = 'kendall'), 'not TRUE') |
... | ... |
@@ -34,25 +44,25 @@ test_that('Inference method calls work', { |
34 | 44 |
}) |
35 | 45 |
|
36 | 46 |
test_that('Correct dimensions of results', { |
37 |
- for (m in dcMethods()) { |
|
47 |
+ for (m in infmethods) { |
|
38 | 48 |
expect_equal(dim(dcScore(x, cond, !!m)), c(4, 4)) |
39 | 49 |
} |
40 | 50 |
}) |
41 | 51 |
|
42 | 52 |
test_that('Attributes attached to results', { |
43 |
- for (m in dcMethods()) { |
|
53 |
+ for (m in infmethods) { |
|
44 | 54 |
expect_equal(attr(dcScore(x, cond, !!m), 'dc.method'), m) |
45 | 55 |
} |
46 | 56 |
}) |
47 | 57 |
|
48 | 58 |
test_that('Diagonals are NAs', { |
49 |
- for (m in dcMethods()) { |
|
59 |
+ for (m in infmethods) { |
|
50 | 60 |
expect_equal(sum(is.na(diag(dcScore(x, cond, !!m)))), nrow(x)) |
51 | 61 |
} |
52 | 62 |
}) |
53 | 63 |
|
54 | 64 |
test_that('Row and column names are the same', { |
55 |
- for (m in dcMethods()) { |
|
65 |
+ for (m in infmethods) { |
|
56 | 66 |
expect_equal(rownames(dcScore(x, cond, !!m)), colnames(dcScore(x, cond, !!m))) |
57 | 67 |
} |
58 | 68 |
}) |