tests/testthat/test_diffusion.R

In cbg-ethz/knockdown: Statistical Analysis of High-Throughput Genetic Perturbation Screens

# perturbatr: analysis of high-throughput gene perturbation screens
#
# Copyright (C) 2018 Simon Dirmeier
#
# This file is part of perturbatr
#
# perturbatr is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# perturbatr is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
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# You should have received a copy of the GNU General Public License
# along with perturbatr If not, see <http://www.gnu.org/licenses/>.


context("diffusion")


data(rnaiscreen)
hm.fit  <- hm(rnaiscreen)

graph <- readRDS(system.file(
  "extdata", "graph_small.rds", package = "perturbatr"))
res <- diffuse(hm.fit, graph=graph, r=0.5)


testthat::test_that("diffusion object prints", {
  testthat::expect_output(show(res))
})


testthat::test_that("diffusion object plots", {
  testthat::expect_silent(s <- plot(res))
})


testthat::test_that("diffusion object returns graph", {
  testthat::expect_true(class(graph(res))[1] == "igraph")
})


testthat::test_that("diffusion object returns params", {
  testthat::expect_true(class(params(res))[1] == "list")
})


testthat::test_that("diffusion object returns data", {
  testthat::expect_true(class(dataSet(res))[1] == "tbl_df")
})


testthat::test_that("diffusion object returns gene effects", {
  testthat::expect_true(class(geneEffects(res))[1] == "tbl_df")
})


testthat::test_that("diffusion object returns bootstrapping boolean", {
  testthat::expect_false(isBootstrapped(res))
})


testthat::test_that("diffusion object returns inference", {
  testthat::expect_true(inference(res) ==
                        perturbatr:::inferenceTypes()$MRW.DIFFUSION)
})