tests/testthat/test-count_unique_geno.R

In qtl2convert: Convert Data among QTL Mapping Packages

context("count_unique_geno")

test_that("count_unique_geno works", {

    g <- rbind(c(NA,  "A",  "A",  "A", "T"),
               c(NA,  NA,   NA,   "A", "A"),
               c("A", "A",  "T",  "G", "G"),
               rep(NA, 5),
               c("N", "H",  "",   "A", "A"),
               c("N", "H",  "",   "A", "T"),
               c("C", "C",  "G",  "G", NA))
    expected <- c(2,1,3,0,1,2,2)
    expect_equal(count_unique_geno(g), expected)

    rownames(g) <- names(expected) <- paste0("mar", 1:7)
    expect_equal(count_unique_geno(g), expected)

})


test_that("count_unique_geno works multi-core", {
    if(isnt_karl()) skip("this test only run locally")

    g <- rbind(c(NA,  "A",  "A",  "A", "T"),
               c(NA,  NA,   NA,   "A", "A"),
               c("A", "A",  "T",  "G", "G"),
               rep(NA, 5),
               c("N", "H",  "",   "A", "A"),
               c("N", "H",  "",   "A", "T"),
               c("C", "C",  "G",  "G", NA))
    expected <- c(2,1,3,0,1,2,2)
    expect_equal(count_unique_geno(g), expected)
    expect_equal(count_unique_geno(g, cores=2), expected)

    rownames(g) <- names(expected) <- paste0("mar", 1:7)
    expect_equal(count_unique_geno(g), expected)
    expect_equal(count_unique_geno(g, cores=2), expected)

})