Nothing
context("compare_genoprob")
test_that("compare_genoprob 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_dir1 <- file.path(tempdir(), "iron_genoprob1")
while(dir.exists(fst_dir1)) {
fst_dir1 <- paste0(fst_dir1, sample(LETTERS, 1))
}
dir.create(fst_dir1)
fst_dir2 <- file.path(tempdir(), "iron_genoprob2")
while(dir.exists(fst_dir2)) {
fst_dir2 <- paste0(fst_dir2, sample(LETTERS, 1))
}
dir.create(fst_dir2)
probs_fst_1 <- calc_genoprob_fst(iron, "iron", fst_dir1, gmap_w_pmar, error_prob=0.002,
overwrite=TRUE)
probs_fst_2 <- calc_genoprob_fst(iron, "iron", fst_dir2, gmap_w_pmar, error_prob=0.2,
overwrite=TRUE)
probs_1 <- fst_extract(probs_fst_1)
probs_2 <- fst_extract(probs_fst_2)
result <- compare_genoprob(probs_1, probs_2, iron, ind=10, chr=2, minmarkers=1, minprob=0.5)
expect_equal(compare_genoprob(probs_fst_1, probs_fst_2, iron, ind=10, chr=2, minmarkers=1, minprob=0.5), result)
expect_equal(compare_genoprob(probs_1, probs_fst_2, iron, ind=10, chr=2, minmarkers=1, minprob=0.5), result)
expect_equal(compare_genoprob(probs_fst_1, probs_2, iron, ind=10, chr=2, minmarkers=1, minprob=0.5), result)
# clean up
unlink(fst_dir1, recursive=TRUE)
unlink(fst_dir2, recursive=TRUE)
})
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