context("readAllelicCountsFile")
vcf.file <- system.file("extdata", "example.vcf.gz", package = "PureCN")
ac.file <- system.file("extdata", "example_allelic_counts.tsv", package = "PureCN")
vcf <- readVcf(vcf.file, "hg19")
data(purecn.example.output)
normal.coverage.file <- system.file('extdata', 'example_normal.txt.gz',
package = 'PureCN')
tumor.coverage.file <- system.file('extdata', 'example_tumor.txt.gz',
package = 'PureCN')
test_that("example parses correctly", {
vcf_ac <- readAllelicCountsFile(ac.file)
expect_equal(as.character(ref(vcf_ac)), as.character(ref(head(vcf,20))))
})
test_that("parsing -> writing -> parsing works", {
output.file <- tempfile(fileext = ".tsv")
PureCN:::.writeAllelicCountsFileGatk(vcf, 1, output.file)
vcf_ac <- readAllelicCountsFile(output.file)
expect_equal(as.character(ref(vcf_ac)), as.character(ref(vcf)))
ret <- runAbsoluteCN(normal.coverage.file = normal.coverage.file,
tumor.coverage.file = tumor.coverage.file,
candidates = purecn.example.output$candidates,
vcf.file = vcf,
genome = "hg19",
test.purity = seq(0.4, 0.7, by = 0.05), min.ploidy = 1.5,
max.ploidy = 2.4, max.candidate.solutions = 1, plot.cnv = FALSE)
expect_true(length(ret$results) > 0)
file.remove(output.file)
})
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