Nothing
context("calc_geno_freq")
test_that("calc_geno_freq works", {
library(qtl2)
# load data and create pseudomarker map
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
gmap_w_pmar <- insert_pseudomarkers(iron$gmap, step=1)
# create directory to hold results
fst_dir <- file.path(tempdir(), "iron_genoprob")
while(dir.exists(fst_dir)) {
fst_dir <- paste0(fst_dir, sample(LETTERS, 1))
}
dir.create(fst_dir)
probs_fst <- calc_genoprob_fst(iron, "iron", fst_dir, gmap_w_pmar, error_prob=0.002,
overwrite=TRUE)
probs <- fst_extract(probs_fst)
expect_equal(calc_geno_freq(probs_fst), calc_geno_freq(probs))
expect_equal(calc_geno_freq(probs_fst, omit_x=FALSE), calc_geno_freq(probs, omit_x=FALSE))
expect_equal(calc_geno_freq(probs_fst, "marker"), calc_geno_freq(probs, "marker"))
expect_equal(calc_geno_freq(probs_fst, "marker", omit_x=FALSE), calc_geno_freq(probs, "marker", omit_x=FALSE))
# clean up
unlink(fst_dir, recursive=TRUE)
})
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