/usr/lib/R/site-library/IRanges/unitTests/test_inter-range-methods.R is in r-bioc-iranges 2.4.1-1.
This file is owned by root:root, with mode 0o644.
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ir1 <- IRanges(c(2,5,1), c(3,7,3))
ir2 <- IRanges(c(5,2,0), c(6,3,1))
checkIdentical(range(ir1), IRanges(1, 7))
checkIdentical(range(ir1, ir2), IRanges(0, 7))
checkIdentical(range(IRanges()), IRanges())
checkException(range(ir1, c(2,3)), silent = TRUE)
}
test_RangesList_range <- function() {
for (compress in c(TRUE, FALSE)) {
rl1 <- IRangesList(a = IRanges(c(1,2),c(4,3)), b = IRanges(c(4,6),c(10,7)),
compress = compress)
rl2 <- IRangesList(c = IRanges(c(0,2),c(4,5)), a = IRanges(c(4,5),c(6,7)),
compress = compress)
ans <- IRangesList(a = IRanges(1,7), b = IRanges(4,10), c = IRanges(0,5),
compress = compress)
checkIdentical(range(rl1, rl2), ans)
names(rl2) <- NULL
ans <- IRangesList(IRanges(0,5), IRanges(4,10), compress = compress)
checkIdentical(range(rl1, rl2), ans)
## must be same length
checkException(range(rl2, rep.int(rl2, 2L)), silent=TRUE)
}
}
test_IRanges_reduce <- function() {
x <- IRanges()
current <- reduce(x)
checkIdentical(x, current)
x <- IRanges(1:3, width=0)
current <- reduce(x, with.revmap=TRUE)
target <- x
mcols(target) <- DataFrame(revmap=as(seq_along(target), "IntegerList"))
checkIdentical(target, current)
current <- reduce(x, drop.empty.ranges=TRUE, with.revmap=TRUE)
target <- IRanges()
mcols(target) <- DataFrame(revmap=as(seq_along(target), "IntegerList"))
checkIdentical(target, current)
x <- IRanges(c(1:4, 10:11, 11), width=c(0,1,1,0,0,0,1))
current <- reduce(x, with.revmap=TRUE)
target <- IRanges(c(1:2, 10:11), width=c(0,2,0,1))
mcols(target) <- DataFrame(revmap=IntegerList(1,2:4,5,6:7))
checkIdentical(target, current)
current <- reduce(x, drop.empty.ranges=TRUE, with.revmap=TRUE)
target <- IRanges(c(2, 11), width=c(2,1))
mcols(target) <- DataFrame(revmap=IntegerList(2:3,7))
checkIdentical(target, current)
x <- IRanges(start=c(1,2,3), end=c(5,2,8))
y <- reduce(x, with.revmap=TRUE)
target <- IRanges(start=1, end=8)
mcols(target) <- DataFrame(revmap=IntegerList(1:3))
checkIdentical(target, y)
mcols(target)$revmap <- as(seq_along(target), "IntegerList")
checkIdentical(target, reduce(y, with.revmap=TRUE))
x <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
y <- reduce(x, with.revmap=TRUE)
target <- IRanges(start=c(1,15,20), end=c(5,15,100))
mcols(target) <- DataFrame(revmap=IntegerList(4, 1, 3:2))
checkIdentical(target, y)
mcols(target)$revmap <- as(seq_along(target), "IntegerList")
checkIdentical(target, reduce(y, with.revmap=TRUE))
x <- IRanges(start=c(7,3,-2,6,7,-10,-2,3), width=c(3,1,0,0,0,0,8,0))
## Before reduction:
## start end width ==-10===-5====0===+5==+10===
## [1] 7 9 3 ....:....:....:....:.xxx:...
## [2] 3 3 1 ....:....:....:..x.:....:...
## [3] -2 -3 0 ....:....:..[.:....:....:...
## [4] 6 5 0 ....:....:....:....:[...:...
## [5] 7 6 0 ....:....:....:....:.[..:...
## [6] -10 -11 0 ....[....:....:....:....:...
## [7] -2 5 8 ....:....:..xxxxxxxx....:...
## [8] 3 2 0 ....:....:....:..[.:....:...
## ---------------------==-10===-5====0===+5==+10===
## After reduction:
## y1: ....[....:..xxxxxxxx.xxx:...
## y3: ....:....:..xxxxxxxx....:...
y1 <- reduce(x)
checkIdentical(y1, IRanges(start=c(-10,-2,7), end=c(-11,5,9)))
checkIdentical(reduce(y1), y1)
y2 <- reduce(x, with.inframe.attrib=TRUE)
checkIdentical(start(attr(y2, "inframe")), c(9L,6L,1L,9L,9L,1L,1L,6L))
checkIdentical(width(attr(y2, "inframe")), width(x))
y3 <- reduce(x, drop.empty.ranges=TRUE)
checkIdentical(y3, y1[width(y1) != 0L])
checkIdentical(reduce(y3), y3)
y4 <- reduce(x, drop.empty.ranges=TRUE, with.inframe.attrib=TRUE)
checkIdentical(attr(y4, "inframe"), attr(y2, "inframe"))
y5 <- reduce(x, min.gapwidth=0)
checkIdentical(y5, IRanges(start=c(-10,-2,-2,6,7,7), end=c(-11,-3,5,5,6,9)))
y6 <- reduce(x, drop.empty.ranges=TRUE, min.gapwidth=0)
checkIdentical(y6, y5[width(y5) != 0L])
y7 <- reduce(x, min.gapwidth=2)
checkIdentical(y7, IRanges(start=c(-10,-2), end=c(-11,9)))
y8 <- reduce(x, min.gapwidth=8)
checkIdentical(y8, y7)
y9 <- reduce(x, min.gapwidth=9)
checkIdentical(y9, IRanges(start=-10, end=9))
}
test_RangesList_reduce <- function() {
range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
range3 <- IRanges(start=c(3,-2,6,7,-10,-2,3), width=c(1,0,0,0,0,8,0))
range4 <- IRanges()
for (compress in c(TRUE, FALSE)) {
collection <- IRangesList(one=range1,
range2,
range3,
range4,
compress=compress)
for (with.revmap in c(FALSE, TRUE)) {
for (drop.empty.ranges in c(FALSE, TRUE)) {
current <- reduce(collection, drop.empty.ranges=drop.empty.ranges,
with.revmap=with.revmap)
target <- IRangesList(one=reduce(range1,
drop.empty.ranges=drop.empty.ranges,
with.revmap=with.revmap),
reduce(range2,
drop.empty.ranges=drop.empty.ranges,
with.revmap=with.revmap),
reduce(range3,
drop.empty.ranges=drop.empty.ranges,
with.revmap=with.revmap),
reduce(range4,
drop.empty.ranges=drop.empty.ranges,
with.revmap=with.revmap),
compress=compress)
checkIdentical(target, current)
}
}
}
}
test_IRanges_gaps <- function() {
checkIdentical(gaps(IRanges()), IRanges())
checkIdentical(gaps(IRanges(), start=1, end=4),
IRanges(start=1, end=4))
x <- IRanges(start=2, end=3)
checkIdentical(gaps(x), IRanges())
checkIdentical(gaps(x, start=2), IRanges())
checkIdentical(gaps(x, start=4), IRanges())
checkIdentical(gaps(x, start=0), IRanges(start=0, end=1))
checkIdentical(gaps(x, end=3), IRanges())
checkIdentical(gaps(x, end=1), IRanges())
checkIdentical(gaps(x, end=5), IRanges(start=4, end=5))
checkIdentical(gaps(x, start=0, end=5), IRanges(start=c(0,4), end=c(1,5)))
}
test_RangesList_gaps <- function() {
range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
for (compress in c(TRUE, FALSE)) {
collection <- IRangesList(one = range1, range2, compress = compress)
checkIdentical(gaps(collection),
IRangesList(one = gaps(range1), gaps(range2),
compress = compress))
}
}
test_Ranges_disjoin <- function()
{
checkIdentical(disjoin(IRanges()), IRanges())
ir <- IRanges(c(1, 1, 4, 10), c(6, 3, 8, 10))
checkIdentical(disjoin(ir), IRanges(c(1, 4, 7, 10), c(3, 6, 8, 10)))
}
test_CompressedIRangesList_disjoin <- function()
{
r0 <- IRanges(10, 20)
checkTrue(validObject(disjoin(IRangesList())))
## unnamed; incl. 0-length
irl <- IRangesList(IRanges())
checkIdentical(irl, disjoin(irl))
irl <- IRangesList(r0, IRanges(), r0)
checkIdentical(irl, disjoin(irl))
irl <- IRangesList(r0, IRanges(), IRanges(), r0)
checkIdentical(irl, disjoin(irl))
## named; incl. 0-length
irl <- IRangesList(a=IRanges())
checkIdentical(irl, disjoin(irl))
irl <- IRangesList(a=r0, b=IRanges(), c=r0)
checkIdentical(irl, disjoin(irl))
irl <- IRangesList(a=r0, b=IRanges(), c=IRanges(), d=r0)
checkIdentical(irl, disjoin(irl))
## no interference between separate elements
r0 <- IRanges(10, c(15, 20))
dr0 <- disjoin(r0)
irl <- IRangesList(r0, r0)
checkIdentical(IRangesList(dr0, dr0), disjoin(irl))
irl <- IRangesList(r0, IRanges(), r0)
checkIdentical(IRangesList(dr0, IRanges(), dr0), disjoin(irl))
## 0-width
## 1-width
r0 <- IRanges(c(1, 10), 10)
irl <- IRangesList(r0, IRanges())
checkIdentical(disjoin(r0), disjoin(irl)[[1]])
irl <- IRangesList(IRanges(), r0)
checkIdentical(disjoin(r0), disjoin(irl)[[2]])
}
test_Ranges_disjointBins <- function()
{
checkIdentical(disjointBins(IRanges()), integer())
checkIdentical(disjointBins(IRanges(1, 5)), 1L)
checkIdentical(disjointBins(IRanges(c(1, 3), c(5, 12))), c(1L, 2L))
checkIdentical(disjointBins(IRanges(c(1, 3, 10), c(5, 12, 13))),
c(1L, 2L, 1L))
checkIdentical(disjointBins(IRanges(c(3, 1, 10), c(5, 12, 13))),
c(2L, 1L, 2L))
}
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