/usr/lib/R/site-library/IRanges/unitTests/test_setops-methods.R is in r-bioc-iranges 2.8.1-1+b1.
This file is owned by root:root, with mode 0o644.
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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 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 | test_IRanges_union <- function() {
x <- IRanges(c(1, 4, 9), c(5, 7, 10))
y <- IRanges(c(2, 2, 10), c(2, 3, 12))
ans <- union(x, y)
ans0 <- IRanges(c(1, 9), c(7, 12))
checkIdentical(ans, ans0)
}
test_IRanges_intersect <- function() {
x <- IRanges(c(1, 4, 9), c(5, 7, 10))
y <- IRanges(c(2, 2, 10), c(2, 3, 12))
ans <- intersect(x, y)
ans0 <- IRanges(c(2,10),c(3,10))
checkIdentical(ans, ans0)
}
test_IRanges_setdiff <- function() {
x <- IRanges(c(1, 4, 9), c(5, 7, 10))
y <- IRanges(c(2, 2, 10), c(2, 3, 12))
ans <- setdiff(x, y)
ans0 <- IRanges(c(1,4,9), c(1,7,9))
checkIdentical(ans, ans0)
ans <- setdiff(y, x)
ans0 <- IRanges(c(11), c(12))
checkIdentical(ans, ans0)
}
test_IRanges_punion <- function() {
x <- IRanges(start=c(1,11,21,31,41,51,61,71), end=c(5,10,25,35,40,55,65,75))
y <- IRanges(start=c(1, 8,18,35,43,48,63,78), end=c(4,15,22,36,45,50,62,79))
ans0 <- IRanges(start=c(1,8,18,31,41,48,61,71), end=c(5,15,25,36,45,55,65,79))
checkIdentical(punion(x, y, fill.gap=TRUE), ans0)
checkIdentical(punion(y, x, fill.gap=TRUE), ans0)
}
test_IRanges_pintersect <- function() {
x <- IRanges(start=c(22,22,22,22,22,22), end=c(28,28,28,28,21,21))
y <- IRanges(start=c(25,30,29,25,22,22), end=c(30,40,40,24,21,29))
ansMaxStart <- IRanges(start=c(25,30,29,25,22,22), end=c(28,29,28,24,21,21))
ansStartX <- IRanges(start=c(25,22,29,25,22,22), end=c(28,21,28,24,21,21))
ansStartY <- IRanges(start=c(25,30,29,25,22,22), end=c(28,29,28,24,21,21))
checkException(pintersect(x, y), silent = TRUE)
checkException(pintersect(y, x), silent = TRUE)
for (resolve.empty in c("none", "max.start", "start.x")) {
checkIdentical(x, pintersect(x, x, resolve.empty = resolve.empty))
checkIdentical(y, pintersect(y, y, resolve.empty = resolve.empty))
}
checkIdentical(pintersect(x[-c(2,3)], y[-c(2,3)]), ansMaxStart[-c(2,3)])
checkIdentical(pintersect(y[-c(2,3)], x[-c(2,3)]), ansMaxStart[-c(2,3)])
checkIdentical(pintersect(x, y, resolve.empty = "max.start"), ansMaxStart)
checkIdentical(pintersect(y, x, resolve.empty = "max.start"), ansMaxStart)
checkIdentical(pintersect(x, y, resolve.empty = "start.x"), ansStartX)
checkIdentical(pintersect(y, x, resolve.empty = "start.x"), ansStartY)
}
test_IRanges_psetdiff <- function() {
x <- IRanges(start=c(1,11,21,31,41,51,61,71), end=c(5,10,25,35,40,55,65,75))
y <- IRanges(start=c(1, 8,18,35,43,48,63,78), end=c(4,15,22,36,45,50,62,79))
ans <- psetdiff(x[-7], y[-7])
ans0 <- IRanges(start=c(5,11,23,31,41,51,71), end=c(5,10,25,34,40,55,75))
checkIdentical(ans, ans0)
ans <- psetdiff(y[-2], x[-2])
ans0 <- IRanges(start=c(1,18,36,43,48,63,78), end=c(0,20,36,45,50,62,79))
checkIdentical(ans, ans0)
}
test_IRanges_pgap <- function() {
x <- IRanges(start=c(1,11,21,31,41,51,61,71), end=c(5,10,25,35,40,55,65,75))
y <- IRanges(start=c(1, 8,18,35,43,48,63,78), end=c(4,15,22,36,45,50,62,79))
ans <- pgap(x, y)
checkIdentical(width(ans), c(0L, 0L, 0L, 0L, 2L, 0L, 0L, 2L))
checkIdentical(start(ans)[width(ans) != 0L], c(41L, 76L))
}
test_RangesList_setops <- function() {
rl1 <- RangesList(IRanges(c(1,2),c(4,3)), IRanges(c(4,6),c(10,7)))
rl2 <- RangesList(IRanges(c(0,2),c(4,5)), IRanges(c(4,5),c(6,7)))
checkIdentical(union(rl1, rl2),
RangesList(union(rl1[[1]], rl2[[1]]), union(rl1[[2]], rl2[[2]])))
checkIdentical(intersect(rl1, rl2),
RangesList(intersect(rl1[[1]], rl2[[1]]), intersect(rl1[[2]], rl2[[2]])))
checkIdentical(setdiff(rl1, rl2),
RangesList(setdiff(rl1[[1]], rl2[[1]]), setdiff(rl1[[2]], rl2[[2]])))
}
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