tests/testthat/test-topNodes.R

In markrobinsonuzh/treeAGG: Tree Aggregation

# context("topNodes")
#
# # assays data
# set.seed(1)
# toyTable <- matrix(rnbinom(40, size = 1, mu = 10), nrow = 10)
# colnames(toyTable) <- paste(rep(LETTERS[1:2], each = 2), rep(1:2, 2), sep = "_")
# rownames(toyTable) <- paste("entity", seq_len(10), sep = "")
#
# data("tinyTree")
# # row data
# rowInf <- DataFrame(var1 = sample(letters[1:2], 10, replace = TRUE),
#                     var2 = sample(c(TRUE, FALSE), 10, replace = TRUE),
#                     nodeLab = tinyTree$tip.label,
#                     row.names = rownames(toyTable))
# # column data
# colInf <- DataFrame(gg = c(1, 2, 3, 3),
#                     group = rep(LETTERS[1:2], each = 2),
#                     row.names = colnames(toyTable))
# # treeSummarizedExperiment
# tse <- treeSummarizedExperiment(assays = list(toyTable),
#                                 rowData = rowInf,
#                                 colData = colInf,
#                                 tree = tinyTree)
# tse <- runEdgeR(obj = tse)
#
# test_that("topNodes could extract results successfully", {
#     expect_is(topNodes(tse, sort.by = "PValue"), "list")
#     expect_equal(dim(topNodes(tse)[[1]][[1]]), c(10, 5))
#     expect_equal(
#         which.max(topNodes(tse, sort.by = "PValue",
#                            decreasing = TRUE)[[1]][[1]][, "PValue"]), 1)
# })