Nothing
context("Correct access and structure of stored database information")
names = read_library_names(ref_gen = "GRCH37")
test_that("show_contained_ccls returns correct object", {
names = read_library_names(ref_gen = "GRCH37")
ccls_all = show_contained_ccls()
expect_is(ccls_all, "data.frame")
expect_equal(dim(ccls_all)[2], 6)
expect_equal(sort(unique(ccls_all$Library)), sort(names))
expect_is(ccls_all[,1], "character")
expect_is(ccls_all[,2], "character")
})
test_that("show_contained_variants_in_library returns correct object", {
names = read_library_names(ref_gen = "GRCH37")
if("CELLMINER" %in% names){
g_ranges = show_contained_variants_in_library(
library_name = "CELLMINER"
)
expect_is(g_ranges, "GRanges")
expect_true(length(g_ranges) > 50000)
expect_equal(sum(grepl("CELLMINER", g_ranges$Member_CCLs)), length(g_ranges))
}
})
test_that("show_contained_variants_for_ccl returns the right object", {
names = read_library_names(ref_gen = "GRCH37")
ccls_all = show_contained_ccls()
if("CELLMINER" %in% names){
index = ccls_all$Library == "CELLMINER"
ccls_all = ccls_all[index,]
ccl_index = sample(1:length(ccls_all), 1, replace = FALSE)
ccl = ccls_all$CCL[ccl_index]
variants = show_contained_variants_for_ccl(
name_ccl = ccl, library_name = "CELLMINER"
)
expect_is(variants, "GRanges")
expect_true(length(variants) > 1)
ccl_index = sample(1:length(ccls_all), 1, replace = FALSE)
ccl = ccls_all$CCL[ccl_index]
variants = show_contained_variants_for_ccl(
name_ccl = ccl, library_name = "CELLMINER"
)
expect_is(variants, "GRanges")
expect_true(length(variants) > 1)
}
})
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