context("Test: bootMatrix() ")


data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)


nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

test_that("is.ExpressionSet() throughs error when no ExpressionSet is entered to bootMatrix()",
          {
                  expect_error(
                          bootMatrix(nonStandardExpressionSet)
                  )
          })


test_that("# permutations matches nrow() of bootMatrix output...", {
        expect_equal(nrow(
                bootMatrix(PhyloExpressionSetExample, permutations = 1)
        ), 1)
        expect_equal(nrow(
                bootMatrix(PhyloExpressionSetExample, permutations = 10)
        ), 10)
        expect_equal(nrow(
                bootMatrix(PhyloExpressionSetExample, permutations = 100)
        ), 100)
        expect_equal(nrow(
                bootMatrix(PhyloExpressionSetExample, permutations = 1000)
        ), 1000)
        
})


test_that("bootMatrix() returns numeric values", {
        expect_true(is.numeric(
                bootMatrix(PhyloExpressionSetExample, permutations = 10)
        ))
})