/usr/lib/R/site-library/IRanges/unitTests/test_IRanges-class.R is in r-bioc-iranges 2.8.1-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | test_IRanges_names <- function() {
range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
checkIdentical(names(range1), NULL)
nms <- c("a", NA, "b")
names(range1) <- nms
checkIdentical(names(range1), nms)
checkTrue(validObject(nms))
names(range1) <- NULL
checkTrue(validObject(nms))
checkIdentical(names(range1), NULL)
names(range1) <- "a"
checkTrue(validObject(range1))
checkIdentical(names(range1), c("a", NA, NA))
checkException(names(range1) <- c("a", "b", "c", "d"), silent = TRUE)
}
test_Ranges_isDisjoint <- function() {
ir1 <- IRanges(c(2,5,1), c(3,7,3))
ir2 <- IRanges(c(2,9,5), c(3,9,6))
ir3 <- IRanges(1, 5)
checkIdentical(isDisjoint(ir1), FALSE)
checkIdentical(isDisjoint(ir2), TRUE)
checkIdentical(isDisjoint(ir3), TRUE)
## Handling of zero-width ranges
current <- sapply(11:17,
function(i)
isDisjoint(IRanges(c(12, i), width=c(4, 0))))
target <- rep(c(TRUE, FALSE, TRUE), c(2, 3, 2))
checkIdentical(target, current)
}
test_IRanges_combine <- function() {
range <- IRanges(start=c(1,2,3,1), end=c(5,2,8,3))
srange <- split(range, start(range) == 1)
checkIdentical(srange,
as(RangesList(`FALSE` = range[2:3], `TRUE` = range[c(1,4)]),
"CompressedIRangesList"))
checkIdentical(do.call(c, unname(as.list(srange))),
IRanges(c(2,3,1,1), c(2,8,5,3)))
ir1 <- IRanges(1, 10)
ir2 <- IRanges(c(1, 15), width=5)
mcols(ir2) <- DataFrame(score=1:2)
checkIdentical(mcols(c(ir1, ir2)),
DataFrame(score = c(NA, 1L, 2L)))
## Combining multiple IRanges object with varying mcols
mcols(ir1) <- DataFrame(gc=0.78)
checkException(c(ir1, ir2), silent=TRUE)
checkIdentical(mcols(c(ir1, ir2, ignore.mcols=TRUE)), NULL)
}
test_IRanges_subset <- function() { # by range
query <- IRanges(c(1, 4, 9), c(5, 7, 10))
subject <- IRanges(c(6, 8, 10), c(7, 12, 14))
checkIdentical(subsetByOverlaps(query, subject), query[2:3])
}
test_IRanges_annotation <- function() {
range <- IRanges(c(1, 4), c(5, 7))
mcols(range) <- DataFrame(a = 1:2)
checkIdentical(mcols(range)[,1], 1:2)
checkIdentical(mcols(range[2:1])[,1], 2:1)
checkIdentical(mcols(c(range,range))[,1], rep(1:2,2))
}
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