tests/testthat/test-CNVMetricMethods.R
In adeschen/CNVMetrics: Copy Number Variant Metrics
### Unit tests for CNVMetricsMethods.R functions
library(CNVMetrics)
library(GenomicRanges)
library(S4Vectors)
library(IRanges)
#############################################################################
### Tests plotMetric() results
#############################################################################
context("plotMetric() results")
test_that("plotMetric() must return error when type not in metric object", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges = IRanges(start=c(100, 300, 800), end=c(200, 500, 900)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData=demo, method="szymkiewicz")
error_message <- paste0("the specified 'type' is not present in ",
"this metric object.")
expect_error(plotMetric(metric=metric, type="SAVE"),
error_message)
})
test_that("plotMetric() must return error when type is an integer", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges = IRanges(start=c(100, 300, 800), end=c(200, 500, 900)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData=demo,
method="szymkiewicz")
error_message <- "the \'type\' must be a single character string"
expect_error(plotMetric(metric=metric, type=33), error_message)
})
test_that("plotMetric() must return error when metric is not CNVMetric object", {
error_message <- "\'metric\' must be a CNVMetric object."
expect_error(plotMetric(metric="TEST01", type="DELETION"),
error_message)
})
test_that("plotMetric() must return error when colorRange is vector of single letters", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800), end = c(200, 500, 900)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000), end = c(250, 700, 1500)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
error_message <- "\'colorRange\' must be be a vector of 2 valid color names."
expect_error(plotMetric(metric=metric, type="AMPLIFICATION",
colorRange=c("a", "b")),
error_message)
})
test_that("plotMetric() must return error when colorRange is vector of one color", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
error_message <- "\'colorRange\' must be a vector of 2 color names."
expect_error(plotMetric(metric=metric, type="AMPLIFICATION",
colorRange=c("red")), error_message)
})
test_that("plotMetric() must return an error when type is not in the CNVMetric object", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("LOH", "LOH", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("LOH", "LOH", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,states = c("LOH"),
method = "szymkiewicz")
error_message <- "the specified \'type\' is not present in this metric object."
expect_error(plotMetric(metric=metric, type="AMPLIFICATION",
colorRange=c("red", "violet")), error_message)
})
test_that("plotMetric() must return error when type==ALL and filename given", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
error_message <- "\'type\' cannot be \'ALL\' when filename argument is used."
expect_error(plotMetric(metric=metric, type="ALL",
filename="test.pdf"), error_message)
})
test_that("plotMetric() must return a gtable when graph for amplification", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
result <- plotMetric(metric=metric, type="AMPLIFICATION")
expect_is(object=result, class="gtable")
})
test_that("plotMetric() must return a gtable when graph for deletion", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
result <- plotMetric(metric=metric, type="DELETION")
expect_is(object=result, class="gtable")
})
test_that("plotMetric() must return a gtable when graph for LOH", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("LOH", "LOH", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("LOH", "LOH", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo, states = "LOH",
method = "jaccard")
result <- plotMetric(metric=metric, type="LOH")
expect_is(object=result, class="gtable")
})
test_that("plotMetric() must return a gtable when graph for log2ratio metric", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31895999)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratio = c(0.3422, 0.5454, -1.4444))
metric <- calculateLog2ratioMetric(demo,
method="weightedEuclideanDistance")
result <- plotMetric(metric=metric)
expect_is(object=result, class="gtable")
})
#############################################################################
### Tests calculateOverlapMetric() results
#############################################################################
context("calculateOverlapMetric() results")
test_that("calculateOverlapMetric() must return error when only one sample present", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- "at least 2 samples must be present in the segmentData"
expect_error(calculateOverlapMetric(segmentData = demo,
method = "sorensen"), error_message)
})
test_that("calculateOverlapMetric() must return error when method is available", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- gettextf("'arg' should be one of %s",
paste(dQuote(c("sorensen", "szymkiewicz")),
collapse = ", "))
expect_error(calculateOverlapMetric(segmentData = demo,
method = "typo"), error_message)
})
test_that("calculateOverlapMetric() must return 1 when two samples identical with sorensen", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
method="sorensen")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, 1, NA), nrow=2, ncol=2,
byrow=TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02")
expected$DELETION <- matrix(c(NA, NA, 1, NA), nrow=2, ncol=2,
byrow=TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02")
rownames(expected$DELETION) <- c("sample01", "sample02")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "sorensen"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return expected results with sorensen", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800),
end = c(200, 500, 900)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000),
end = c(250, 700, 1500)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample03"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(50, 600, 1000),
end = c(250, 700, 2000)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
method="sorensen")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, NA, 0.202380952380952, NA, NA,
0.334437086092715, 0.801587301587302, NA), nrow=3, ncol=3,
byrow=TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
expected$DELETION <- matrix(c(NA, NA, NA, 0, NA, NA,
0, 0.667110519307590, NA), nrow=3, ncol=3, byrow=TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02", "sample03")
rownames(expected$DELETION) <- c("sample01", "sample02", "sample03")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "sorensen"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return expected results with szymkiewicz", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800),
end = c(200, 500, 900)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000),
end = c(250, 700, 1500)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample03"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(50, 600, 1000),
end = c(250, 700, 2000)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
metho="szymkiewicz")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, NA, 0.252475247524752, NA, NA,
0.334437086092715, 1.000000000000000, NA),
nrow = 3, ncol = 3, byrow = TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
expected$DELETION <- matrix(c(NA, NA, NA, 0.000000000000000, NA, NA,
0.000000000000000, 1.000000000000000, NA),
nrow = 3, ncol = 3,
byrow = TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02", "sample03")
rownames(expected$DELETION) <- c("sample01", "sample02", "sample03")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "szymkiewicz"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return expected results with jaccard", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800),
end = c(200, 500, 900)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000),
end = c(250, 700, 1500)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample03"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(50, 600, 1000),
end = c(250, 700, 2000)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
metho="jaccard")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, NA, 0.112582781456954, NA, NA,
0.200795228628231, 0.668874172185430, NA),
nrow = 3, ncol = 3, byrow = TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
expected$DELETION <- matrix(c(NA, NA, NA, 0.000000000000000, NA, NA,
0.000000000000000, 0.500499500499501, NA),
nrow = 3, ncol = 3,
byrow = TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02", "sample03")
rownames(expected$DELETION) <- c("sample01", "sample02", "sample03")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "jaccard"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return an error when segmentData has only one sample", {
error_message <- "at least 2 samples must be present in the segmentData"
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
expect_error(calculateOverlapMetric(demo), error_message)
})
test_that("calculateOverlapMetric() must return an error when segmentData has metadata status instead of state", {
error_message <- paste0("at least one sample doesn't have a metadata column ",
"called \'state\'")
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
status = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
status= c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
expect_error(calculateOverlapMetric(demo), error_message)
})
test_that("calculateOverlapMetric() must return an error when segmentData doesn't have metadata state", {
error_message <- paste0("at least one sample doesn't have a metadata column ",
"called \'state\'")
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)),
strand = "*")
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)),
strand = "*")
expect_error(calculateOverlapMetric(demo), error_message)
})
test_that("calculateOverlapMetric() must return an error when states is a vector of integers", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- paste0("the \'states\' argument must be a ",
"vector of strings with at least one value")
expect_error(calculateOverlapMetric(segmentData = demo, states = c(33, 11),
method="sorensen"), error_message)
})
test_that("calculateOverlapMetric() must return an error when states is an empty vector", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- paste0("the \'states\' argument must be a ",
"vector of strings with at least one value")
expect_error(calculateOverlapMetric(segmentData = demo, states = c(),
method="sorensen"), error_message)
})
test_that("calculateOverlapMetric() must return an error when segmentData is a list", {
demo <- list()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- paste0("the \'segmentData\' argument must be a",
" \'GRangesList\' object")
expect_error(calculateOverlapMetric(segmentData = demo,
states = c("AMPLIFICATION"),
method="sorensen"), error_message)
})
#############################################################################
### Tests calculateLog2ratioMetric() results
#############################################################################
context("calculateLog2ratioMetric() results")
test_that("calculateLog2ratioMetric() must return an error when segmentData is a list", {
demo <- list()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratio = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'segmentData\' argument must be a",
" \'GRangesList\' object")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when segmentData has only one sample", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
error_message <- "at least 2 samples must be present in segmentData"
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when segmentData doesn't have a log2ratio column", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratios = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratios = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("at least one sample doesn't have a metadata ",
"column called \'log2ratio\'")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when minThreshold is negative value", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratios = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratios = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'minThreshold\' argument must be a ",
"positive numeric value")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=-0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when minThreshold is a string", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratios = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratios = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'minThreshold\' argument must be a ",
"positive numeric value")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold="0.01",
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when excludedRegions is a string", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratio = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'excludedRegions\' argument must ",
"a \'Granges\' object or NULL")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.4,
excludedRegions="hello"), error_message)
})
adeschen/CNVMetrics documentation built on July 19, 2023, 10:24 p.m.
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### Unit tests for CNVMetricsMethods.R functions
library(CNVMetrics)
library(GenomicRanges)
library(S4Vectors)
library(IRanges)
#############################################################################
### Tests plotMetric() results
#############################################################################
context("plotMetric() results")
test_that("plotMetric() must return error when type not in metric object", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges = IRanges(start=c(100, 300, 800), end=c(200, 500, 900)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData=demo, method="szymkiewicz")
error_message <- paste0("the specified 'type' is not present in ",
"this metric object.")
expect_error(plotMetric(metric=metric, type="SAVE"),
error_message)
})
test_that("plotMetric() must return error when type is an integer", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges = IRanges(start=c(100, 300, 800), end=c(200, 500, 900)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData=demo,
method="szymkiewicz")
error_message <- "the \'type\' must be a single character string"
expect_error(plotMetric(metric=metric, type=33), error_message)
})
test_that("plotMetric() must return error when metric is not CNVMetric object", {
error_message <- "\'metric\' must be a CNVMetric object."
expect_error(plotMetric(metric="TEST01", type="DELETION"),
error_message)
})
test_that("plotMetric() must return error when colorRange is vector of single letters", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800), end = c(200, 500, 900)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000), end = c(250, 700, 1500)),
strand = "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
error_message <- "\'colorRange\' must be be a vector of 2 valid color names."
expect_error(plotMetric(metric=metric, type="AMPLIFICATION",
colorRange=c("a", "b")),
error_message)
})
test_that("plotMetric() must return error when colorRange is vector of one color", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
error_message <- "\'colorRange\' must be a vector of 2 color names."
expect_error(plotMetric(metric=metric, type="AMPLIFICATION",
colorRange=c("red")), error_message)
})
test_that("plotMetric() must return an error when type is not in the CNVMetric object", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("LOH", "LOH", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("LOH", "LOH", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,states = c("LOH"),
method = "szymkiewicz")
error_message <- "the specified \'type\' is not present in this metric object."
expect_error(plotMetric(metric=metric, type="AMPLIFICATION",
colorRange=c("red", "violet")), error_message)
})
test_that("plotMetric() must return error when type==ALL and filename given", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
error_message <- "\'type\' cannot be \'ALL\' when filename argument is used."
expect_error(plotMetric(metric=metric, type="ALL",
filename="test.pdf"), error_message)
})
test_that("plotMetric() must return a gtable when graph for amplification", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
result <- plotMetric(metric=metric, type="AMPLIFICATION")
expect_is(object=result, class="gtable")
})
test_that("plotMetric() must return a gtable when graph for deletion", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo,
method = "szymkiewicz")
result <- plotMetric(metric=metric, type="DELETION")
expect_is(object=result, class="gtable")
})
test_that("plotMetric() must return a gtable when graph for LOH", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(100, 300, 800), end = c(200, 500, 900)),
strand="*", state=c("LOH", "LOH", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames="chr1",
ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)),
strand="*", state=c("LOH", "LOH", "DELETION"))
metric <- calculateOverlapMetric(segmentData = demo, states = "LOH",
method = "jaccard")
result <- plotMetric(metric=metric, type="LOH")
expect_is(object=result, class="gtable")
})
test_that("plotMetric() must return a gtable when graph for log2ratio metric", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31895999)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratio = c(0.3422, 0.5454, -1.4444))
metric <- calculateLog2ratioMetric(demo,
method="weightedEuclideanDistance")
result <- plotMetric(metric=metric)
expect_is(object=result, class="gtable")
})
#############################################################################
### Tests calculateOverlapMetric() results
#############################################################################
context("calculateOverlapMetric() results")
test_that("calculateOverlapMetric() must return error when only one sample present", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- "at least 2 samples must be present in the segmentData"
expect_error(calculateOverlapMetric(segmentData = demo,
method = "sorensen"), error_message)
})
test_that("calculateOverlapMetric() must return error when method is available", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- gettextf("'arg' should be one of %s",
paste(dQuote(c("sorensen", "szymkiewicz")),
collapse = ", "))
expect_error(calculateOverlapMetric(segmentData = demo,
method = "typo"), error_message)
})
test_that("calculateOverlapMetric() must return 1 when two samples identical with sorensen", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
method="sorensen")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, 1, NA), nrow=2, ncol=2,
byrow=TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02")
expected$DELETION <- matrix(c(NA, NA, 1, NA), nrow=2, ncol=2,
byrow=TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02")
rownames(expected$DELETION) <- c("sample01", "sample02")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "sorensen"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return expected results with sorensen", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800),
end = c(200, 500, 900)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000),
end = c(250, 700, 1500)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample03"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(50, 600, 1000),
end = c(250, 700, 2000)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
method="sorensen")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, NA, 0.202380952380952, NA, NA,
0.334437086092715, 0.801587301587302, NA), nrow=3, ncol=3,
byrow=TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
expected$DELETION <- matrix(c(NA, NA, NA, 0, NA, NA,
0, 0.667110519307590, NA), nrow=3, ncol=3, byrow=TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02", "sample03")
rownames(expected$DELETION) <- c("sample01", "sample02", "sample03")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "sorensen"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return expected results with szymkiewicz", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800),
end = c(200, 500, 900)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000),
end = c(250, 700, 1500)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample03"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(50, 600, 1000),
end = c(250, 700, 2000)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
metho="szymkiewicz")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, NA, 0.252475247524752, NA, NA,
0.334437086092715, 1.000000000000000, NA),
nrow = 3, ncol = 3, byrow = TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
expected$DELETION <- matrix(c(NA, NA, NA, 0.000000000000000, NA, NA,
0.000000000000000, 1.000000000000000, NA),
nrow = 3, ncol = 3,
byrow = TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02", "sample03")
rownames(expected$DELETION) <- c("sample01", "sample02", "sample03")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "szymkiewicz"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return expected results with jaccard", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(100, 300, 800),
end = c(200, 500, 900)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(150, 600, 1000),
end = c(250, 700, 1500)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample03"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(50, 600, 1000),
end = c(250, 700, 2000)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
result <- calculateOverlapMetric(segmentData=demo,
metho="jaccard")
expected <- list()
expected$AMPLIFICATION <- matrix(c(NA, NA, NA, 0.112582781456954, NA, NA,
0.200795228628231, 0.668874172185430, NA),
nrow = 3, ncol = 3, byrow = TRUE)
colnames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
rownames(expected$AMPLIFICATION) <- c("sample01", "sample02", "sample03")
expected$DELETION <- matrix(c(NA, NA, NA, 0.000000000000000, NA, NA,
0.000000000000000, 0.500499500499501, NA),
nrow = 3, ncol = 3,
byrow = TRUE)
colnames(expected$DELETION) <- c("sample01", "sample02", "sample03")
rownames(expected$DELETION) <- c("sample01", "sample02", "sample03")
class(expected) <- "CNVMetric"
attr(expected, 'metric') <- "jaccard"
expect_equal(result, expected)
})
test_that("calculateOverlapMetric() must return an error when segmentData has only one sample", {
error_message <- "at least 2 samples must be present in the segmentData"
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
expect_error(calculateOverlapMetric(demo), error_message)
})
test_that("calculateOverlapMetric() must return an error when segmentData has metadata status instead of state", {
error_message <- paste0("at least one sample doesn't have a metadata column ",
"called \'state\'")
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
status = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
status= c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
expect_error(calculateOverlapMetric(demo), error_message)
})
test_that("calculateOverlapMetric() must return an error when segmentData doesn't have metadata state", {
error_message <- paste0("at least one sample doesn't have a metadata column ",
"called \'state\'")
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)),
strand = "*")
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)),
strand = "*")
expect_error(calculateOverlapMetric(demo), error_message)
})
test_that("calculateOverlapMetric() must return an error when states is a vector of integers", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- paste0("the \'states\' argument must be a ",
"vector of strings with at least one value")
expect_error(calculateOverlapMetric(segmentData = demo, states = c(33, 11),
method="sorensen"), error_message)
})
test_that("calculateOverlapMetric() must return an error when states is an empty vector", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- paste0("the \'states\' argument must be a ",
"vector of strings with at least one value")
expect_error(calculateOverlapMetric(segmentData = demo, states = c(),
method="sorensen"), error_message)
})
test_that("calculateOverlapMetric() must return an error when segmentData is a list", {
demo <- list()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
error_message <- paste0("the \'segmentData\' argument must be a",
" \'GRangesList\' object")
expect_error(calculateOverlapMetric(segmentData = demo,
states = c("AMPLIFICATION"),
method="sorensen"), error_message)
})
#############################################################################
### Tests calculateLog2ratioMetric() results
#############################################################################
context("calculateLog2ratioMetric() results")
test_that("calculateLog2ratioMetric() must return an error when segmentData is a list", {
demo <- list()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratio = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'segmentData\' argument must be a",
" \'GRangesList\' object")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when segmentData has only one sample", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
error_message <- "at least 2 samples must be present in segmentData"
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when segmentData doesn't have a log2ratio column", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratios = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratios = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("at least one sample doesn't have a metadata ",
"column called \'log2ratio\'")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when minThreshold is negative value", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratios = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratios = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'minThreshold\' argument must be a ",
"positive numeric value")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=-0.2,
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when minThreshold is a string", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratios = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratios = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'minThreshold\' argument must be a ",
"positive numeric value")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold="0.01",
excludedRegions=NULL), error_message)
})
test_that("calculateLog2ratioMetric() must return an error when excludedRegions is a string", {
demo <- GRangesList()
demo[["sample01"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1905048, 4554832, 31686841),
end = c(2004603, 4577608, 31695808)), strand = "*",
log2ratio = c(2.5555, 1.9932, -0.9999))
demo[["sample02"]] <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1995066, 31611222, 31690000),
end = c(2204505, 31689898, 31895666)), strand = c("-", "+", "+"),
log2ratio = c(0.3422, 0.5454, -1.4444))
error_message <- paste0("the \'excludedRegions\' argument must ",
"a \'Granges\' object or NULL")
expect_error(calculateLog2ratioMetric(segmentData = demo,
method="weightedEuclideanDistance", minThreshold=0.4,
excludedRegions="hello"), error_message)
})
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