/usr/lib/R/site-library/IRanges/unitTests/test_RangesList-class.R is in r-bioc-iranges 2.8.1-1+b1.
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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 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 | test_RangesList_construction <- function() {
empty <- RangesList()
checkTrue(validObject(empty))
checkIdentical(length(empty), 0L)
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))
named <- RangesList(one = range1, two = range2)
checkTrue(validObject(named))
checkIdentical(length(named), 2L)
checkIdentical(start(named),
IntegerList(one = start(range1), two = start(range2),
compress=FALSE))
checkIdentical(end(named),
IntegerList(one = end(range1), two = end(range2),
compress=FALSE))
checkIdentical(width(named),
IntegerList(one = width(range1), two = width(range2),
compress=FALSE))
checkIdentical(names(named), c("one", "two"))
checkIdentical(range1, named[[1]])
unnamed <- RangesList(range1, range2)
checkTrue(validObject(unnamed))
checkIdentical(length(unnamed), 2L)
checkIdentical(range2, unnamed[[2]])
checkIdentical(names(unnamed), NULL)
}
test_RangesList_subset <- function() { ## by RangesList
range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
range2 <- IRanges(start=c(1,15,20,45), end=c(5,15,100,80))
collection <- RangesList(one = range1, range2)
checkIdentical(subsetByOverlaps(collection, RangesList()),
RangesList(one=IRanges(), IRanges()))
checkIdentical(subsetByOverlaps(collection,
RangesList(IRanges(4, 6), IRanges(50, 70))),
RangesList(one=IRanges(c(1,3),c(5,8)),
IRanges(c(20,45),c(100,80))))
checkIdentical(subsetByOverlaps(collection,
RangesList(IRanges(50, 70), one=IRanges(4, 6))),
RangesList(one=IRanges(c(1,3),c(5,8)), IRanges()))
}
test_RangesList_as_list <- 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))
checkIdentical(list(range1, range2),
as.list(RangesList(range1, range2)))
checkIdentical(list(a=range1, b=range2),
as.list(RangesList(a=range1, b=range2)))
}
test_RangesList_as_data_frame <- 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))
rl <- RangesList(range1, range2)
df <- data.frame(group=togroup(PartitioningByWidth(rl)),
group_name=NA_character_,
as.data.frame(c(range1,range2)), stringsAsFactors=FALSE)
checkIdentical(df, as.data.frame(rl))
names(rl) <- c("a", "b")
df$group_name <- c("a", "b")[togroup(PartitioningByWidth(rl))]
checkIdentical(df, as.data.frame(rl))
}
test_IRangesList_construction <- 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)) {
named <- IRangesList(one = range1, two = range2, compress = compress)
checkIdentical(length(named), 2L)
checkIdentical(names(named), c("one", "two"))
checkIdentical(range1, named[[1]])
unnamed <- IRangesList(range1, range2)
checkTrue(validObject(unnamed))
checkIdentical(length(unnamed), 2L)
checkIdentical(range2, unnamed[[2]])
checkIdentical(names(unnamed), NULL)
}
}
test_IRangesList_annotation <- 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)) {
rl <- IRangesList(range1, range2, compress = compress)
mcols(rl) <- DataFrame(a = 1:2)
checkIdentical(mcols(rl)[,1], 1:2)
checkIdentical(mcols(rl[2:1])[,1], 2:1)
checkIdentical(mcols(c(rl,rl))[,1], rep(1:2,2))
checkIdentical(mcols(append(rl,rl))[,1], rep(1:2,2))
}
}
## test_RangesList_overlap <- function() {
## rl1 <- RangesList(a = IRanges(c(1,2),c(4,3)), b = IRanges(c(4,6),c(10,7)))
## rl2 <- RangesList(b = IRanges(c(0,2),c(4,5)), a = IRanges(c(4,5),c(6,7)))
## overlap(rl1, rl2)
## overlap(rl1, rl2, select = "first")
## overlap(rl1, rl2, select = "first", drop = TRUE)
## names(rl2)[1] <- "c"
## overlap(rl1, rl2)
## overlap(rl1, rl2, select = "first")
## overlap(rl1, rl2, select = "first", drop = TRUE)
## names(rl2) <- NULL
## overlap(rl1, rl2)
## overlap(rl1, rl2, select = "first")
## overlap(rl1, rl2, select = "first", drop = TRUE)
## overlap(rl1, rl2[1])
## overlap(rl1, rl2[1], select = "first")
## overlap(rl1, rl2[1], select = "first", drop = TRUE)
## overlap(rl1[1], rl2)
## overlap(rl1[1], rl2, select = "first")
## overlap(rl1[1], rl2, select = "first", drop = TRUE)
## }
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