Nothing
context("processMultipleSamples")
test_that("example output correct", {
normal1.coverage.file <- system.file("extdata", "example_normal.txt",
package="PureCN")
normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
package="PureCN")
tumor1.coverage.file <- system.file("extdata", "example_tumor.txt",
package="PureCN")
tumor2.coverage.file <- system.file("extdata", "example_tumor2.txt",
package="PureCN")
normal.coverage.files <- c(normal1.coverage.file, normal2.coverage.file)
tumor.coverage.files <- c(tumor1.coverage.file, tumor2.coverage.file)
normalDB <- createNormalDatabase(normal.coverage.files)
pool <- calculateTangentNormal(tumor1.coverage.file, normalDB)
seg <- processMultipleSamples(tumor.coverage.files,
sampleids = c("Sample1", "Sample2"),
normalDB = normalDB,
genome = "hg19")
expect_equal(c("Sample1", "Sample2"), levels(seg[,1]))
seg2 <- processMultipleSamples(
list(tumor.coverage.files[1],readCoverageFile(tumor.coverage.files[2])),
sampleids = c("Sample1", "Sample2"),
normalDB = normalDB,
genome = "hg38", plot.cnv = FALSE)
expect_equal(c("Sample1", "Sample2"), levels(seg2[,1]))
seg.file <- tempfile(fileext = ".seg")
write.table(seg, seg.file, row.names = FALSE, sep = "\t")
vcf.file <- system.file("extdata", "example.vcf.gz", package = "PureCN")
ret <- runAbsoluteCN(tumor.coverage.file = tumor1.coverage.file,
normal.coverage.file = pool,
seg.file = seg.file, vcf.file = vcf.file, max.candidate.solutions = 1,
fun.segmentation = segmentationHclust, post.optimize = TRUE,
genome = "hg19", min.ploidy = 1.5, max.ploidy = 2.1,
test.purity = seq(0.4, 0.7, by = 0.05), sampleid = "Sample1")
expect_equal(0.65, ret$results[[1]]$purity)
expect_error(processMultipleSamples(tumor.coverage.files,
sampleids = c("Sample1", "Sample2"),
normalDB = normalDB,
genome = "hg20"), "centromere")
})
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