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
|
test_that("test_ceScan", {
axtFnHg38DanRer10 <- file.path(system.file("extdata", package="CNEr"),
"hg38.danRer10.net.axt")
axtHg38DanRer10 <- readAxt(axtFnHg38DanRer10)
axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
axtDanRer10Hg38 <- readAxt(axtFnDanRer10Hg38)
bedHg38Fn <- file.path(system.file("extdata", package="CNEr"),
"filter_regions.hg38.bed")
bedHg38 <- readBed(bedHg38Fn)
bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"),
"filter_regions.danRer10.bed")
bedDanRer10 <- readBed(bedDanRer10Fn)
skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg38")
skip_if_not_installed("BSgenome.Drerio.UCSC.danRer10")
library(BSgenome.Drerio.UCSC.danRer10)
library(BSgenome.Hsapiens.UCSC.hg38)
qSizesHg38 <- seqinfo(BSgenome.Hsapiens.UCSC.hg38)
qSizesDanRer10 <- seqinfo(BSgenome.Drerio.UCSC.danRer10)
windows <- c(50L, 50L, 50L)
identities <- c(45L, 48L, 49L)
CNEHg38DanRer10 <- ceScan(x=axtHg38DanRer10, tFilter=bedHg38,
qFilter=bedDanRer10,
tSizes=qSizesHg38, qSizes=qSizesDanRer10,
window=windows, identity=identities)
# check the names of CNE list
expect_identical(names(CNEHg38DanRer10), c("45_50", "48_50", "49_50"))
# check the CNEs in "45_50" set
expect_identical(length(CNEHg38DanRer10[["45_50"]]), 4L)
targetCNEs <- GRanges(seqnames=c("chr3"),
ranges=IRanges(start=c(137523038, 137523122,
137269941, 137264717),
end=c(137523102, 137523187,
137269991, 137265124)),
strand="+", seqinfo=qSizesHg38)
expect_identical(first(CNEHg38DanRer10[["45_50"]]), targetCNEs)
queryCNEs <- GRanges(seqnames=c("chr6"),
ranges=IRanges(start=c(26638744, 26638826,
26746284, 26745047),
end=c(26638808, 26638891,
26746334, 26745455)),
strand="+", seqinfo=qSizesDanRer10)
expect_identical(last(CNEHg38DanRer10[["45_50"]]), queryCNEs)
library(S4Vectors)
mcolsCNEs <- DataFrame(score=c(87.69, 89.39, 90.20, 95.11),
cigar=c("65M", "66M", "51M", "218M1D190M"))
expect_identical(mcols(CNEHg38DanRer10[["45_50"]]), mcolsCNEs)
}
)
|
