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
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
|
context("test-read_vcfs_as_granges")
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(BSgenome)
library(ref_genome, character.only = TRUE)
sample_names <- c(
"colon1", "colon2", "colon3",
"intestine1", "intestine2", "intestine3",
"liver1", "liver2", "liver3"
)
vcfs <- list.files(system.file("extdata", package = "MutationalPatterns"),
pattern = "sample.vcf", full.names = TRUE
)
# Test default
test_that("loads multiple samples", {
output <- read_vcfs_as_granges(vcfs, sample_names, ref_genome)
expect_that(length(output), equals(9))
expect_true(inherits(output, "CompressedGRangesList"))
})
# Test for seqlevel filters
test_that("nuclear filter works", {
output <- read_vcfs_as_granges(vcfs, sample_names, ref_genome)
expected <- c(
"chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7",
"chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14",
"chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21",
"chr22", "chrX", "chrY"
)
expect_that(seqlevels(output), equals(expected))
})
test_that("autosomal filter works", {
output <- read_vcfs_as_granges(vcfs, sample_names, ref_genome, "auto")
expected <- c(
"chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7",
"chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14",
"chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21",
"chr22"
)
expect_that(seqlevels(output), equals(expected))
})
test_that("unfiltered works", {
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)
output <- read_vcfs_as_granges(vcfs, sample_names, ref_genome, "none")
expected <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15",
"chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22",
"chrX", "chrY", "chrM", "GL000207.1", "GL000226.1", "GL000229.1",
"GL000231.1", "GL000210.1", "GL000239.1", "GL000235.1", "GL000201.1",
"GL000247.1", "GL000245.1", "GL000197.1", "GL000203.1", "GL000246.1",
"GL000249.1", "GL000196.1", "GL000248.1", "GL000244.1", "GL000238.1",
"GL000202.1", "GL000234.1", "GL000232.1", "GL000206.1", "GL000240.1",
"GL000236.1", "GL000241.1", "GL000243.1", "GL000242.1", "GL000230.1",
"GL000237.1", "GL000233.1", "GL000204.1", "GL000198.1", "GL000208.1",
"GL000191.1", "GL000227.1", "GL000228.1", "GL000214.1", "GL000221.1",
"GL000209.1", "GL000218.1", "GL000220.1", "GL000213.1", "GL000211.1",
"GL000199.1", "GL000217.1", "GL000216.1", "GL000215.1", "GL000205.1",
"GL000219.1", "GL000224.1", "GL000223.1", "GL000195.1", "GL000212.1",
"GL000222.1", "GL000200.1", "GL000193.1", "GL000194.1", "GL000225.1",
"GL000192.1")
expect_equal(seqlevels(output), expected)
})
# Test that a warning is given when vcf and names lengths don't match
test_that("An error is given when vcf and names lengths don't match", {
expect_error(
{
read_vcfs_as_granges(vcfs, sample_names[1:8], ref_genome)
},
"Please provide the same number of sample names as VCF files"
)
})
# Test that a warning is given when the supplied reference is not a BSgenome object
test_that("An error is given when the supplied ref is not a BSgenome object", {
expect_error(
{
read_vcfs_as_granges(vcfs, sample_names, "a")
},
"Please provide the name of a BSgenome object."
)
})
# Test that you can read in specific mutation types
vcf_fnames <- list.files(system.file("extdata", package = "MutationalPatterns"),
pattern = "blood.*vcf", full.names = TRUE
)
sample_names <- c("AC", "ACC55", "BCH")
test_that("indels work", {
output <- read_vcfs_as_granges(vcf_fnames, sample_names, ref_genome, type = "indel")
expect_that(length(output), equals(3))
expect_true(inherits(output, "CompressedGRangesList"))
})
test_that("dbs work", {
output <- read_vcfs_as_granges(vcf_fnames, sample_names, ref_genome, type = "dbs")
expect_that(length(output), equals(3))
expect_true(inherits(output, "CompressedGRangesList"))
})
output <- read_vcfs_as_granges(vcf_fnames, sample_names, ref_genome, type = "mbs")
test_that("mbs work", {
expect_that(length(output), equals(3))
expect_true(inherits(output, "CompressedGRangesList"))
})
test_that("all mutation types work", {
output <- read_vcfs_as_granges(vcf_fnames, sample_names, ref_genome, type = "all")
expect_that(length(output), equals(3))
expect_true(inherits(output, "CompressedGRangesList"))
})
test_that("predefined_dbs_mbs argument works", {
output <- read_vcfs_as_granges(vcf_fnames,
sample_names,
ref_genome,
type = "dbs",
predefined_dbs_mbs = TRUE)
expect_that(length(output), equals(3))
expect_that(as.double(S4Vectors::elementNROWS(output)), equals(c(0, 0, 0)))
expect_true(inherits(output, "CompressedGRangesList"))
})
# Test function works on an empty vcf
empty_vcf <- list.files(system.file("extdata", package = "MutationalPatterns"),
pattern = "empty.vcf", full.names = TRUE
)
test_that("Empty vcf works", {
expect_warning(
{
output <- read_vcfs_as_granges(empty_vcf, "empty", ref_genome)
},
"There were 0 variants \\(before filtering\\) found in the vcf file"
)
expect_true(inherits(output, "CompressedGRangesList"))
expect_equal(length(output[[1]]), 0)
})
# Test that it is possible to keep duplicate variants
duplicate_vcf <- list.files(system.file("extdata", package = "MutationalPatterns"),
pattern = "duplicate.vcf", full.names = TRUE
)
test_that("Empty vcf works", {
output <- read_vcfs_as_granges(duplicate_vcf, "duplicate", ref_genome, remove_duplicate_variants = F)
expect_true(inherits(output, "CompressedGRangesList"))
expect_equal(length(output[[1]]), 2)
})
|
