Nothing
context("Scale kinship matrix")
test_that("scale_kinship works for RIL", {
set.seed(49265251)
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
map <- insert_pseudomarkers(grav2$gmap, step=1)
probs <- calc_genoprob(grav2, map, error_prob=0.002)
sim <- calc_kinship(probs)
scaled <- scale_kinship(sim)
# row and colnames okay
expect_equal(dimnames(scaled), dimnames(sim))
# check some values
expect_equal(diag(scaled), setNames(rep(1, nrow(sim)), colnames(sim)))
d <- sqrt(diag(sim))
n <- 10
pairs <- matrix(sample(ncol(sim), 2*n, replace=TRUE), ncol=2)
for(i in 1:n)
expect_equal(scaled[pairs[i,1], pairs[i,2]],
setNames(sim[pairs[i,1], pairs[i,2]] / (d[pairs[i,1]] * d[pairs[i,2]]), NULL) )
# test with "loco" method
sim_loco <- calc_kinship(probs, "loco")
scaled_loco <- scale_kinship(sim_loco)
expected <- sim_loco
for(i in seq_along(sim_loco))
expected[[i]] <- scale_kinship(sim_loco[[i]])
expect_equal(scaled_loco, expected)
})
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