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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)),
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 <- "coverage"
for (fun in generic_functions) {
generic <- getGeneric(fun)
method <- getMethod(fun, "RangedSummarizedExperiment")
checkIdentical("x", generic@signature)
checkIdentical(formals(generic@.Data), formals(method@.Data))
}
}
test_coverage_RangedSummarizedExperiment <- function()
{
for (i in 1:2) {
x <- rseList[[i]]
target <- coverage(rowRanges(x))
current <- coverage(x)
checkIdentical(target, current)
weight <- runif(length(x))
## Issues a warning (in BioC 3.3) when rowRanges(x) is a GRangesList
## object, which reveals a problem with how the "coverage" method for
## GRangesList objects handles the 'weight' argument. The warning is
## expected and healthy, don't try to suppress it here. It will go
## away when we fix the "coverage" method for GRangesList objects
## (defined in the GenomicRanges package).
target <- coverage(rowRanges(x), weight=weight)
current <- coverage(x, weight=weight)
checkIdentical(target, current)
}
}
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