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
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
|
###
M1 <- matrix(1, 5, 3)
M2 <- matrix(1, 3, 3)
assaysList <- list(gr=SimpleList(m=M1), grl=SimpleList(m=M2))
rowRangesList <-
list(gr=GRanges("chr1", IRanges(1:5, 10)),
grl=split(GRanges("chr1", IRanges(1:5, 10)), c(1,1,2,2,3)))
names(rowRangesList[["grl"]]) <- NULL
colData <- DataFrame(x=letters[1:3])
## a list of one SE with GRanges and one with GRangesList
rseList <-
list(SummarizedExperiment(
assays=assaysList[["gr"]],
rowRanges=rowRangesList[["gr"]],
colData=colData),
SummarizedExperiment(
assays=assaysList[["grl"]],
rowRanges=rowRangesList[["grl"]],
colData=colData))
test_interfaces <- function()
{
fun <- "findOverlaps"
signatures <- list(
c("RangedSummarizedExperiment", "Vector"),
c("Vector", "RangedSummarizedExperiment"),
c("RangedSummarizedExperiment", "RangedSummarizedExperiment")
)
generic <- getGeneric(fun)
for (sig in signatures) {
method <- getMethod(fun, sig)
checkIdentical(c("query", "subject"), generic@signature)
checkIdentical(formals(generic@.Data), formals(method@.Data))
}
}
test_findOverlaps_methods <- function()
{
identical_SummarizedExperiment <- function(x, y) {
x@assays <- as(assays(x), "SimpleAssays")
y@assays <- as(assays(y), "SimpleAssays")
identical(x, y)
}
for (i in 1:2) {
x <- rseList[[i]]
for (j in 1:2) {
y <- rseList[[j]]
## findOverlaps
target <- findOverlaps(rowRanges(x), rowRanges(y))
current <- findOverlaps(x, rowRanges(y))
checkIdentical(target, current)
current <- findOverlaps(rowRanges(x), y)
checkIdentical(target, current)
current <- findOverlaps(x, y)
checkIdentical(target, current)
## countOverlaps
target <- countOverlaps(rowRanges(x), rowRanges(y))
current <- countOverlaps(x, rowRanges(y))
checkIdentical(target, current)
current <- countOverlaps(rowRanges(x), y)
checkIdentical(target, current)
current <- countOverlaps(x, y)
checkIdentical(target, current)
## overlapsAny
target <- overlapsAny(rowRanges(x), rowRanges(y))
current <- overlapsAny(x, rowRanges(y))
checkIdentical(target, current)
current <- overlapsAny(rowRanges(x), y)
checkIdentical(target, current)
current <- overlapsAny(x, y)
checkIdentical(target, current)
## subsetByOverlaps
target <- subsetByOverlaps(x, rowRanges(y))
current <- subsetByOverlaps(x, rowRanges(y))
checkTrue(identical_SummarizedExperiment(target, current))
current <- subsetByOverlaps(x, y)
checkTrue(identical_SummarizedExperiment(target, current))
target <- subsetByOverlaps(rowRanges(x), rowRanges(y))
current <- subsetByOverlaps(rowRanges(x), y)
checkIdentical(target, current)
}
}
}
|
