tests/testthat/test_summary_table.R

In regsplice: L1-regularization based methods for detection of differential splicing

library(regsplice)
context("Summary table")

test_that("summary table function works correctly", {
  
  # generate data
  set.seed(123)
  n_exons <- c(7, 18, 5, 5, 1, 3, 11)
  counts <- matrix(sample(100:200, sum(n_exons) * 6, replace = TRUE), ncol = 6)
  gene_IDs <- paste0("gene", 1:length(n_exons))
  condition <- rep(c(0, 1), each = 3)
  
  rs_data <- RegspliceData(counts, gene_IDs, n_exons, condition)
  
  rs_results <- regsplice(rs_data)
  
  table_default             <- summaryTable(rs_results)
  table_all_up_to_threshold <- summaryTable(rs_results, n = Inf)
  table_all                 <- summaryTable(rs_results, n = Inf, threshold = 1)
  
  table_pval <- summaryTable(rs_results, rank_by = "p-value")
  table_none <- summaryTable(rs_results, rank_by = "none")
  
  table_small_default <- summaryTable(rs_results, n = 3)
  table_small_pval    <- summaryTable(rs_results, n = 3, rank_by = "p-value")
  table_small_none    <- summaryTable(rs_results, n = 3, rank_by = "none")
  
  
  expect_equal(ncol(table_default), 5)
  expect_equal(ncol(table_all_up_to_threshold), 5)
  expect_equal(nrow(table_all), 6)
  expect_equal(ncol(table_all), 5)
  
  expect_equal(ncol(table_pval), 5)
  expect_equal(nrow(table_none), 6)
  expect_equal(ncol(table_none), 5)
  
  expect_equal(ncol(table_small_default), 5)
  expect_equal(ncol(table_small_pval), 5)
  expect_equal(nrow(table_small_none), 3)
  expect_equal(ncol(table_small_none), 5)
})