context("Copy number variation (CNV) calling")
test_that("cnv returns correct output", {
if(require(brassicaData) && require(DNAcopy)){
data("raw_napus", package = "brassicaData")
raw_napus <- filt_samp(raw_napus, raw_napus$samples[-(1:200)])
raw_napus <- filt_snps(raw_napus, raw_napus$snps[-(1:20)])
dat <- intens_theta(raw_napus)
dat <- remove_suffix(dat, "_Grn")
dat <- geno_baf_rratio(dat, delthresh = 11)
dat <- filt_snps(dat, dat$snps[is.na(rowMeans(dat$baf, na.rm = TRUE))])
set.seed(31415)
dat <- segm(dat)
dat <- cnv(dat, dup = 0.03, del = -0.06)
expect_equal(class(dat), "norm_data")
expect_true(is.list(dat))
expect_true(is.matrix(dat$cnv))
expect_equal(dim(dat$cnv), c(12,100))
}
})
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