Nothing
context("calculation of grid positions")
suppressMessages(library(qtl))
test_that("grid-based version works in simple case", {
# equally-spaced map
map <- seq(0, 50, by=2.5)
names(map) <- paste0("map", seq(along=map))
# step = marker distance
pmap <- insert_pseudomarkers(list("1"=map), step=2.5, off_end=0, stepwidth="fixed")
grid <- calc_grid(list("1"=map), step=2.5, off_end=0)
expect_equal(length(pmap[[1]]), length(grid[[1]]))
expect_equal(names(pmap[[1]]), names(grid[[1]]))
expected_grid <- rep(TRUE, length(map))
names(expected_grid) <- names(map)
expect_equal(grid, list("1"=expected_grid))
# step = 1
pmap <- insert_pseudomarkers(list("1"=map), step=1, off_end=0, stepwidth="fixed")
grid <- calc_grid(list("1"=map), step=1, off_end=0)
# expected grid
expected_grid <- !is.na(match(pmap[[1]], seq(0, 50, by=1)))
names(expected_grid) <- names(pmap[[1]])
expect_equal(grid, list("1"=expected_grid))
})
test_that("minimal version works in simple case", {
# equally-spaced map
map <- seq(0, 50, by=2.5)
names(map) <- paste0("map", seq(along=map))
# step = marker distance
grid <- calc_grid(list("1"=map), step=2.5, off_end=0)
expected_grid <- rep(TRUE, length(map))
names(expected_grid) <- names(map)
expect_equal(grid, list("1"=expected_grid))
})
test_that("insert_pseudomarkers gives distinct pseudomarker names with iron data", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
pmap <- insert_pseudomarkers(iron$gmap, step=1)
grid <- calc_grid(iron$gmap, step=1)
expect_equal(length(pmap), length(grid))
expect_equal(names(pmap), names(grid))
for(i in seq(along=pmap)) {
expect_equal(length(pmap[[i]]), length(grid[[i]]))
expect_equal(names(pmap[[i]]), names(grid[[i]]))
}
})
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