context("Test: omitMatrix() ")

data(PhyloExpressionSetExample)

# adapted from: https://github.com/hadley/dplyr/blob/master/tests/testthat/test-arrange.r
equal_df <- function(df1, df2) {
        rownames(df1) <- NULL
        rownames(df2) <- NULL
        colnames(df1) <- NULL
        colnames(df2) <- NULL
        isTRUE(all.equal(df1, df2))
}

nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

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


TestOmitMatrix <- omitMatrix(PhyloExpressionSetExample)[1:50 ,]
TestOmitMatrix2 <- matrix(NA_real_, 50, 7)
colnames(TestOmitMatrix2) <- names(PhyloExpressionSetExample)[3:9]
rownames(TestOmitMatrix2) <-
        paste0("(-) ", PhyloExpressionSetExample[1:50, 2])

for (i in 1:50)
        TestOmitMatrix2[i,] <-
        TAI(PhyloExpressionSetExample[-c(i),])

test_that("omitMatrix() computes correct TAI/TDI values", {
        expect_true(equal_df(TestOmitMatrix, TestOmitMatrix2))
        
})