Nothing
context("DGEobj.utils - tests for extractCol.R functions")
skip_if(setup_failed)
test_that('extractCol: extractCol()', {
extractCol_contrastList <- getType(t_obj1, "topTable")[1:2]
extractCol_one_test <- extractCol(extractCol_contrastList, colName = "P.Value")
expect_true(is.data.frame(extractCol_one_test))
expect_equal(nrow(extractCol_one_test), 951)
expect_equal(ncol(extractCol_one_test), 2)
expect_equal(names(extractCol_one_test), c("BDL_vs_Sham", "EXT1024_vs_BDL"))
extractCol_two_test <- extractCol(extractCol_contrastList, colName = "P.Value", robust = FALSE)
expect_true(is.data.frame(extractCol_two_test))
expect_equal(nrow(extractCol_two_test), 951)
expect_equal(ncol(extractCol_two_test), 2)
expect_equal(names(extractCol_two_test), c("BDL_vs_Sham", "EXT1024_vs_BDL"))
expect_error(extractCol(extractCol_three_test),
regexp = "object 'extractCol_three_test' not found")
# Testing assert
## contrastList
msg <- "contrastList must be a list of data.frames which all have the same colnames and same row counts."
dataframe1 <- getType(t_obj1, "topTable")[[3]][1:10,]
extractCol_contrastList2 <- extractCol_contrastList
extractCol_contrastList2$dataframe1 <- dataframe1
dataframe2 <- getType(t_obj1, "topTable")[[3]]
extractCol_contrastList3 <- extractCol_contrastList
colnames(dataframe2) <- 1:length(dataframe2)
extractCol_contrastList3$dataframe2 <- dataframe2
expect_error(extractCol(),
regexp = msg)
expect_error(extractCol(contrastList = NULL),
regexp = msg)
expect_error(extractCol(contrastList = extractCol_contrastList2),
regexp = msg)
expect_error(extractCol(contrastList = extractCol_contrastList3),
regexp = msg)
## robust
msg <- "robust must be a singular logical value. Assigning default value TRUE."
expect_warning(extractCol(extractCol_contrastList, colName = "P.Value",
robust = NULL),
regexp = msg)
expect_warning(extractCol(extractCol_contrastList, colName = "P.Value",
robust = "FALSE"),
regexp = msg)
expect_warning(extractCol(extractCol_contrastList, colName = "P.Value",
robust = c(FALSE, FALSE)),
regexp = msg)
})
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