Nothing
context("correctCoverageBias")
normal.coverage.file <- system.file("extdata", "example_normal.txt",
package = "PureCN")
interval.file <- system.file("extdata", "ex2_intervals.txt",
package = "PureCN", mustWork = TRUE)
interval.file2 <- system.file("extdata", "example_intervals.txt",
package = "PureCN")
test_that("Example data matches after normalization", {
output.file <- tempfile(fileext = ".txt")
coverage <- correctCoverageBias(normal.coverage.file, interval.file2,
output.file = output.file)
expect_equal(class(coverage)[1], "GRanges")
expect_equal(length(coverage), 10049)
correctCoverageBias(normal.coverage.file, interval.file2, plot.max.density = 100,
plot.bias = TRUE)
x <- readCoverageFile(output.file)
expect_equal(x$average.coverage, coverage$average.coverage)
correctCoverageBias(head(x, 200), interval.file2)
gc.data <- read.delim(interval.file2, as.is = TRUE)
gc.data$Gene <- NULL
tmpFile <- tempfile()
write.table(gc.data, file = tmpFile, row.names = FALSE, quote = FALSE,
sep = "\t")
coverage2 <- correctCoverageBias(normal.coverage.file, tmpFile,
output.file = output.file)
corCov <- cor(coverage$average.coverage, coverage2$average.coverage,
use = "complete.obs")
expect_true(corCov > 0.99)
})
test_that("Exceptions happen with wrong input", {
expect_error(correctCoverageBias(normal.coverage.file, interval.file))
coverage <- readCoverageFile(normal.coverage.file)
coverage$average.coverage <- 0
expect_error(correctCoverageBias(coverage, interval.file), "zero")
})
test_that("Example data qc matches", {
output.qc.file <- tempfile(fileext = ".txt")
coverage <- correctCoverageBias(normal.coverage.file, interval.file2,
output.qc.file = output.qc.file)
x <- read.delim(output.qc.file, sep=" ")
expect_equal(1, nrow(x))
expect_equal(10, ncol(x))
file.remove(output.qc.file)
})
test_that("Example data without reptiming works", {
x <- read.delim(interval.file2)
interval.file3 <- tempfile(fileext = ".txt")
x$reptiming <- NULL
write.table(x, file=interval.file3, row.names=FALSE, quote=FALSE, sep="\t")
coverage <- correctCoverageBias(normal.coverage.file, interval.file3,
plot.bias=TRUE)
expect_equal(nrow(x), length(coverage))
file.remove(interval.file3)
})
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