tests/testthat/test-HRDetect.R
In pdiakumis/hrdetect: Signature Tools
context("testing HRDetect pipeline")
test_that("test HRDetect_pipeline() to make sure it raises an error when the input data matrix is not properly formatted.", {
data_matrix <- NULL
expect_error(res <- HRDetect_pipeline(data_matrix))
})
test_that("test HRDetect_pipeline() runs correctly on two samples.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
col_hrdetect <- c("del.mh.prop", "SNV3", "SV3", "SV5", "hrd", "SNV8")
data_matrix <- matrix(NA,nrow = length(sample_names),ncol = length(col_hrdetect),dimnames = list(sample_names,col_hrdetect))
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(data_matrix,
genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
nparallel = 2)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on one sample.", {
sample_names <- c("test_hrdetect_1")
col_hrdetect <- c("del.mh.prop", "SNV3", "SV3", "SV5", "hrd", "SNV8")
data_matrix <- matrix(NA,nrow = length(sample_names),ncol = length(col_hrdetect),dimnames = list(sample_names,col_hrdetect))
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(data_matrix,
genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
nparallel = 1)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on one sample with Breast signatures and no data_matrix provided.", {
sample_names <- c("test_hrdetect_1")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
nparallel = 1)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on two samples with Breast signatures and no data_matrix provided.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
nparallel = 2)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on one sample with Breast signatures and no data_matrix provided and with bootstrap.", {
sample_names <- c("test_hrdetect_1")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
bootstrap_scores = TRUE,
nparallel = 1)
#if no error happen this code can be reached
expect_true(nrow(res$q_5_50_95)==1)
})
test_that("test HRDetect_pipeline() runs correctly on two samples with Breast signatures and no data_matrix provided and with bootstrap.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
bootstrap_scores = TRUE,
nparallel = 2)
#if no error happen this code can be reached
expect_true(nrow(res$q_5_50_95)==2)
})
test_that("test HRDetect_pipeline() runs correctly on two samples with subset of COSMIC signatures.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
col_hrdetect <- c("del.mh.prop", "SNV3", "SV3", "SV5", "hrd", "SNV8")
data_matrix <- matrix(NA,nrow = length(sample_names),ncol = length(col_hrdetect),dimnames = list(sample_names,col_hrdetect))
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(data_matrix,
genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "COSMIC",
cosmic_siglist = c(1,2,3,8,13),
nparallel = 2)
#if no error happen this code can be reached
expect_true(TRUE)
})
pdiakumis/hrdetect documentation built on May 17, 2020, 5:30 p.m.
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context("testing HRDetect pipeline")
test_that("test HRDetect_pipeline() to make sure it raises an error when the input data matrix is not properly formatted.", {
data_matrix <- NULL
expect_error(res <- HRDetect_pipeline(data_matrix))
})
test_that("test HRDetect_pipeline() runs correctly on two samples.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
col_hrdetect <- c("del.mh.prop", "SNV3", "SV3", "SV5", "hrd", "SNV8")
data_matrix <- matrix(NA,nrow = length(sample_names),ncol = length(col_hrdetect),dimnames = list(sample_names,col_hrdetect))
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(data_matrix,
genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
nparallel = 2)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on one sample.", {
sample_names <- c("test_hrdetect_1")
col_hrdetect <- c("del.mh.prop", "SNV3", "SV3", "SV5", "hrd", "SNV8")
data_matrix <- matrix(NA,nrow = length(sample_names),ncol = length(col_hrdetect),dimnames = list(sample_names,col_hrdetect))
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(data_matrix,
genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
nparallel = 1)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on one sample with Breast signatures and no data_matrix provided.", {
sample_names <- c("test_hrdetect_1")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
nparallel = 1)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on two samples with Breast signatures and no data_matrix provided.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
nparallel = 2)
#if no error happen this code can be reached
expect_true(TRUE)
})
test_that("test HRDetect_pipeline() runs correctly on one sample with Breast signatures and no data_matrix provided and with bootstrap.", {
sample_names <- c("test_hrdetect_1")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
bootstrap_scores = TRUE,
nparallel = 1)
#if no error happen this code can be reached
expect_true(nrow(res$q_5_50_95)==1)
})
test_that("test HRDetect_pipeline() runs correctly on two samples with Breast signatures and no data_matrix provided and with bootstrap.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "Breast",
bootstrap_scores = TRUE,
nparallel = 2)
#if no error happen this code can be reached
expect_true(nrow(res$q_5_50_95)==2)
})
test_that("test HRDetect_pipeline() runs correctly on two samples with subset of COSMIC signatures.", {
sample_names <- c("test_hrdetect_1","test_hrdetect_2")
col_hrdetect <- c("del.mh.prop", "SNV3", "SV3", "SV5", "hrd", "SNV8")
data_matrix <- matrix(NA,nrow = length(sample_names),ncol = length(col_hrdetect),dimnames = list(sample_names,col_hrdetect))
SNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.snv.simple.txt",
"test_hrdetect_2/test_hrdetect_2.snv.simple.txt")
names(SNV_tab_files) <- sample_names
SV_bedpe_files <- c("test_hrdetect_1/test_hrdetect_1.sv.bedpe",
"test_hrdetect_2/test_hrdetect_2.sv.bedpe")
names(SV_bedpe_files) <- sample_names
Indels_vcf_files <- c("test_hrdetect_1/test_hrdetect_1.indel.vcf.gz",
"test_hrdetect_2/test_hrdetect_2.indel.vcf.gz")
names(Indels_vcf_files) <- sample_names
CNV_tab_files <- c("test_hrdetect_1/test_hrdetect_1.cna.txt",
"test_hrdetect_2/test_hrdetect_2.cna.txt")
names(CNV_tab_files) <- sample_names
res <- HRDetect_pipeline(data_matrix,
genome.v = "hg19",
SNV_tab_files = SNV_tab_files,
SV_bedpe_files = SV_bedpe_files,
Indels_vcf_files = Indels_vcf_files,
CNV_tab_files = CNV_tab_files,
signature_type = "COSMIC",
cosmic_siglist = c(1,2,3,8,13),
nparallel = 2)
#if no error happen this code can be reached
expect_true(TRUE)
})
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