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
|
.noGaps <- GAlignments(
Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
c(1, 3, 2, 4)),
pos=1:10, cigar=paste0(10:1, "M"),
strand=Rle(strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
names=head(letters, 10), score=1:10)
.Gaps <- GAlignments(
Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
strand=Rle(strand(c("-", "+")), c(4, 3)),
names=tail(letters, 7), score=1:7)
GAList <- GAlignmentsList(a=.noGaps, b=.Gaps)
quiet <- suppressWarnings
test_GAlignmentsList_construction <- function() {
checkTrue(validObject(GAlignmentsList()))
checkTrue(validObject(new("GAlignmentsList")))
checkTrue(validObject(GAlignmentsList(.noGaps, .Gaps)))
checkTrue(validObject(GAlignmentsList(GAlignments())))
checkTrue(validObject(GAlignmentsList(a=GAlignments())))
checkException(GAlignmentsList(GRanges()), silent = TRUE)
}
test_GAlignmentsList_coercion <- function() {
galist <- GAlignmentsList(a=.noGaps[seqnames(.noGaps) == "chr3"],
b=.Gaps[seqnames(.Gaps) == "chr4"])
## Lists
rgl <- rglist(galist)
grl <- grglist(galist)
checkIdentical(length(rgl), length(galist))
checkIdentical(length(grl), length(galist))
checkIdentical(elementLengths(rgl), elementLengths(grl))
checkIdentical(elementLengths(rgl)[1], elementLengths(galist)[1])
checkIdentical(elementLengths(grl)[1], elementLengths(galist)[1])
## Ranges
checkIdentical(length(ranges(galist)),
length(ranges(galist[1])) +
length(ranges(galist[2])))
checkIdentical(length(quiet(granges(galist))),
length(quiet(granges(galist[1]))) +
length(quiet(granges(galist[2]))))
checkIdentical(length(granges(galist, ignore.strand=TRUE)),
length(granges(galist[1], ignore.strand=TRUE)) +
length(granges(galist[2], ignore.strand=TRUE)))
gr <- granges(galist, ignore.strand=TRUE)
ir <- ranges(galist)
checkIdentical(length(gr), length(ir))
gr <- quiet(granges(galist, ignore.strand=FALSE))
checkTrue(length(gr) == 4L)
## data.frame
df <- data.frame(element=rep(c("a", "b"), each=2),
seqnames=c("chr1", rep("chr2", 3)),
strand=c("-", "+", "-", "-"),
cigar=c("10M", "9M", "5M", "3M2N3M2N3M"),
qwidth=c(10, 9 , 5, 9), start=c(1, 2, 1, 2),
end=c(10, 10, 5, 14), width=c(10, 9, 5, 13),
njunc=c(0, 0, 0, 2), score=c(1, 2, 1, 2),
row.names=c("a", "b", "t", "u"),
stringsAsFactors=FALSE)
galist <- GAlignmentsList(a=.noGaps[1:2], b=.Gaps[1:2])
checkTrue(all.equal(as.data.frame(galist), df))
## introns
galist <- GAList
grl <- junctions(galist)
checkIdentical(names(galist), names(grl))
checkTrue(length(galist) == length(grl))
checkTrue(length(grl[[1]]) == 0L)
checkTrue(length(grl[[2]]) == 4L)
}
test_GAlignmentsList_accessors <- function() {
galist <- GAlignmentsList(.noGaps, .Gaps)
target <- RleList(lapply(GAList, seqnames), compress=TRUE)
checkIdentical(seqnames(GAList), target)
target <- RleList(lapply(GAList, rname), compress=TRUE)
checkIdentical(rname(GAList), target)
target <- CharacterList(lapply(GAList, cigar), compress=TRUE)
checkIdentical(cigar(GAList), target)
target <- RleList(lapply(GAList, strand), compress=TRUE)
checkIdentical(strand(GAList), target)
target <- IntegerList(lapply(GAList, width))
checkIdentical(width(GAList), target)
target <- SplitDataFrameList(lapply(GAList, mcols))
checkIdentical(mcols(GAList, level="within"), target)
}
test_GAlignmentsList_subset_combine <- function()
{
galist <- GAList
score <- 1:length(togroup(galist))
meta <- DataFrame(score=score, more=score+10)
mcols(galist@unlistData) <- meta
## 'c'
checkIdentical(GAlignmentsList(),
c(GAlignmentsList(), GAlignmentsList()))
checkIdentical(GAlignmentsList(.noGaps, .Gaps),
quiet(c(GAlignmentsList(.noGaps), GAlignmentsList(.Gaps))))
## '['
checkIdentical(galist, galist[])
checkIdentical(galist, galist[Rle(TRUE)])
checkIdentical(galist[c(TRUE, FALSE),], galist[1])
}
|
