Nothing
context("recode_snps")
test_that("recode_snps works", {
skip_if(isnt_karl(), "this test only run locally")
# load example data
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
pr <- calc_genoprob(DOex, error_prob=0.002, cores=2)
nmis_ind <- n_missing(DOex)
nmis_mar <- n_missing(DOex, "mar")
DOex <- recode_snps(DOex)
# no change in number missing
expect_equal(nmis_ind, n_missing(DOex))
expect_equal(nmis_mar, n_missing(DOex, "mar"))
# no change in genotype probabilities
expect_equal(pr, calc_genoprob(DOex, error_prob=0.002, cores=2))
fg <- do.call("cbind", DOex$founder_geno)
fg[fg!=1 & fg!=3] <- NA
expect_true(all(colMeans(fg==1, na.rm=TRUE) >= 0.5))
})
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