/usr/lib/R/site-library/GenomicRanges/unitTests/test_GIntervalTree-class.R is in r-bioc-genomicranges 1.14.3-1.
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 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 | make_gr <- function()
{
seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
GRanges(seqnames =
Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges = IRanges(
1:10, width = 10:1, names = head(letters,10)),
strand = Rle(
strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
score = 1:10,
GC = seq(1, 0, length=10),
seqinfo=seqinfo)
}
test_GIntervalTree_fully_specified_coercion <- function() {
gr=make_gr()
git=as(gr,"GIntervalTree")
checkIdentical(seqinfo(git), seqinfo(gr))
checkIdentical(seqnames(git), seqnames(gr))
checkIdentical(strand(git), strand(gr))
}
test_GIntervalTree_fully_specified_constructor <- function() {
gr=make_gr()
git <- GIntervalTree(gr)
checkIdentical(seqinfo(git), seqinfo(gr))
checkIdentical(seqnames(git), seqnames(gr))
checkIdentical(strand(git), strand(gr))
}
test_GIntervalTree_partial_coercion <- function() {
gr <- GRanges(seqnames=rep(c("chr1","chr2"),len=10), ranges=IRanges(start=1:10, width=100))
git=as(gr,"GIntervalTree")
checkIdentical(seqinfo(git), seqinfo(gr))
checkIdentical(seqnames(git), seqnames(gr))
checkIdentical(strand(git), strand(gr))
}
test_GIntervalTree_conversion_to_GRanges <- function () {
gr <- GRanges(seqnames=rep(c("chr1","chr2"),len=10),
ranges=IRanges(start=1:10, width=100),
strand=rep(c("+","-"), len=10), a=letters[1:10])
gr2 <- as(as(gr,"GIntervalTree"), "GRanges")
checkIdentical(gr,gr2)
}
test_GIntervalTree_subsetting <- function () {
gr <- GRanges(seqnames=rep(c("chr1","chr2"),len=10),
ranges=IRanges(start=1:10, width=100),
strand=rep(c("+","-"), len=10), a=letters[1:10])
git=as(gr,"GIntervalTree")
gr <- gr[4:7,]
git <- git[4:7,]
checkIdentical(seqinfo(git), seqinfo(gr))
checkIdentical(seqnames(git), seqnames(gr))
checkIdentical(strand(git), strand(gr))
}
test_GIntervalTree_findOverlaps <- function() {
subject <-
GRanges(seqnames =
Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges =
IRanges(1:10, width = 10:1, names = head(letters,10)),
strand =
Rle(strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
score = 1:10,
GC = seq(1, 0, length=10))
query <-
GRanges(seqnames = "chr2", ranges = IRanges(4:3, 6),
strand = "+", score = 5:4, GC = 0.45)
stree <- GIntervalTree(subject)
olaps2=findOverlaps(query, subject)
olaps1=findOverlaps(query, stree)
checkIdentical(olaps1, olaps2)
}
test_GIntervalTree_subsetByOverlaps <- function() {
subject <-
GRanges(seqnames =
Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges =
IRanges(1:10, width = 10:1, names = head(letters,10)),
strand =
Rle(strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
score = 1:10,
GC = seq(1, 0, length=10))
query <-
GRanges(seqnames = "chr2", ranges = IRanges(4:3, 6),
strand = "+", score = 5:4, GC = 0.45)
stree <- as(subject,"GIntervalTree")
olaps2 <- subsetByOverlaps(query, subject)
olaps1 <- subsetByOverlaps(query, stree)
checkIdentical(olaps1,olaps2)
}
|