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###
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), Rle(c("+", "-"), 3:2)),
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()
{
generic_functions <- c("isDisjoint", "disjointBins")
for (fun in generic_functions) {
generic <- getGeneric(fun)
method <- getMethod(fun, "RangedSummarizedExperiment")
checkIdentical("x", generic@signature)
checkIdentical(formals(generic@.Data), formals(method@.Data))
}
}
test_inter_range_methods <- function()
{
#for (i in 1:2) {
for (i in 1L) {
x <- rseList[[i]]
## isDisjoint
target <- isDisjoint(rowRanges(x))
current <- isDisjoint(x)
checkIdentical(target, current)
## disjointBins
target <- disjointBins(rowRanges(x))
current <- disjointBins(x)
checkIdentical(target, current)
}
}
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