tests/testthat/test-functions.R

In MahShaaban/aacna: Analysis Compendium of the Autophagy and AMPK Co-expression

context("functions")

test_that('test expression_subset', {
  library(Biobase)
  data("sample.ExpressionSet")
  pd <- pData(sample.ExpressionSet)

  set.seed(123)
  byrow <- sample(c(TRUE, FALSE), nrow(sample.ExpressionSet), replace = TRUE)
  bycol <- pd$sex == 'Female'

  mat <- expression_subset(sample.ExpressionSet, byrow, bycol)

  expect_equal(dim(mat), c(sum(byrow), sum(bycol)))

  # test collapsing rows
  set.seed(123)
  rowGroup <- sample(LETTERS, nrow(sample.ExpressionSet), replace = TRUE)

  mat <- expression_subset(sample.ExpressionSet,
                           collapse_rows = TRUE, rowGroup = rowGroup,
                           rowID = featureNames(sample.ExpressionSet))

  expect_equal(dim(mat), c(ncol(sample.ExpressionSet)[[1]], length(unique(rowGroup))))
})

test_that('test expression_reshape', {
  library(Biobase)
  data("sample.ExpressionSet")

  mat <- exprs(sample.ExpressionSet)

  dat <- expression_reshape(mat)

  expect_true(all(dim(dat$data) == dim(mat)[2:1]))
})

test_that('test metadata_get', {
  library(Biobase)
  data("sample.ExpressionSet")

  df <- metadata_get(sample.ExpressionSet, c('sex', 'type'), c('sex', 'type'))

  expect_equal(dim(df), c(ncol(sample.ExpressionSet)[[1]], 3))
})


test_that('test cna_run', {
  library(Biobase)
  data("sample.ExpressionSet")
  dat <- list(data = t(exprs(sample.ExpressionSet)))

  cna <- cna_run(dat$data, power = 5)

  expect_equal(length(cna), 9)
  expect_equal(length(cna$colors), nrow(sample.ExpressionSet)[[1]])
})