Nothing
context("test-parse-variants")
#
## filter_variants_by_standard_chromosomes
#
with_mock_api({
test_that("filter_variants_by_standard_chromosomes: no non-standard locations", {
my_variants <- get_variants(variant_id = c('rs3798440', 'rs7329174'))
expect_is(my_variants, 'variants')
my_variants2 <- filter_variants_by_standard_chromosomes(my_variants)
expect_equal(my_variants, my_variants2)
})
})
with_mock_api({
test_that("filter_variants_by_standard_chromosomes: mitochondrial locations", {
my_variants <- get_variants(variant_id = c('rs147903261', 'rs267606894'))
expect_is(my_variants, 'variants')
my_variants2 <- filter_variants_by_standard_chromosomes(my_variants)
# By default filter_variants_by_standard_chromosomes should preserve variants
# mapped to on the mitochondrial (MT) genome.
expect_identical(my_variants, my_variants2)
})
})
with_mock_api({
test_that("filter_variants_by_standard_chromosomes: drop mitochondrial locations", {
my_variants <- get_variants(variant_id = c('rs147903261', 'rs267606894'))
expect_is(my_variants, 'variants')
# Only allow autosomal and sex chromosomes (exclude the mitochondrial chr).
my_variants2 <- filter_variants_by_standard_chromosomes(my_variants, chromosomes = c(1:22, 'X', 'Y'))
expect_identical(my_variants2, variants())
})
})
# Variants that also map to scaffolds other than the normal chromosomes
# rs10910092: maps to chr 1 and to CHR_HSCHR1_1_CTG3.
# rs570398477: maps to chr 2 and to CHR_HSCHR2_4_CTG1.
with_mock_api({
test_that("filter_variants_by_standard_chromosomes: non-standard locations are dropped", {
my_variants <- get_variants(variant_id = c('rs10910092', 'rs570398477'))
expect_is(my_variants, 'variants')
my_variants2 <- filter_variants_by_standard_chromosomes(my_variants)
expect_identical(nrow(my_variants2@variants), 2L)
})
})
test_that("filter_variants_by_standard_chromosomes: exceptions", {
expect_error(filter_variants_by_standard_chromosomes(chromosomes = 'blah'), "These are not valid chromosome names: blah.")
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.