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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("shift", "narrow", "resize",
"flank", "promoters",
"restrict", "trim")
for (fun in generic_functions) {
generic <- getGeneric(fun)
method <- getMethod(fun, "RangedSummarizedExperiment")
checkIdentical("x", generic@signature)
checkIdentical(formals(generic@.Data), formals(method@.Data))
}
}
test_intra_range_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) {
for (i in 1L) {
## shift
target <- rseList[[i]]
rowRanges(target) <- shift(rowRanges(target), 50)
current <- shift(rseList[[i]], 50)
checkTrue(identical_SummarizedExperiment(target, current))
## narrow
target <- rseList[[i]]
rowRanges(target) <- narrow(rowRanges(target), 2, -2)
current <- narrow(rseList[[i]], 2, -2)
checkTrue(identical_SummarizedExperiment(target, current))
## resize
target <- rseList[[i]]
rowRanges(target) <- resize(rowRanges(target), 8)
current <- resize(rseList[[i]], 8)
checkTrue(identical_SummarizedExperiment(target, current))
## flank
target <- rseList[[i]]
rowRanges(target) <- flank(rowRanges(target), 5, both=TRUE)
current <- flank(rseList[[i]], 5, both=TRUE)
checkTrue(identical_SummarizedExperiment(target, current))
## promoters
target <- rseList[[i]]
rowRanges(target) <- promoters(rowRanges(target),
upstream=20, downstream=5)
current <- promoters(rseList[[i]], upstream=20, downstream=5)
checkTrue(identical_SummarizedExperiment(target, current))
## restrict
target <- rseList[[i]]
rowRanges(target) <- restrict(rowRanges(target), start=2, end=3,
keep.all.ranges=TRUE)
current <- restrict(rseList[[i]], start=2, end=3,
keep.all.ranges=TRUE)
checkTrue(identical_SummarizedExperiment(target, current))
## trim
suppressWarnings(seqlengths(rseList[[i]]) <- 8)
target <- rseList[[i]]
rowRanges(target) <- trim(rowRanges(target))
current <- trim(rseList[[i]])
checkTrue(identical_SummarizedExperiment(target, current))
seqlengths(rseList[[i]]) <- NA
}
}
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