tests/testthat/test-utils.R

In insilico/Rinbix: Insilico Bioinformatics Toolbox

library(Rinbix)
library(expm)

context("Utilities")

data("testdata100ME4")

test_that("fisherRtoZ check range from -1 to 1", {
  testValues <- seq(from = -0.9, to = 0.9, by = 0.25)
  lapply(testValues, function(x) { expect_equal(fisherRtoZ(x), 0.5 * log((1 + x) / (1 - x))) })
})

test_that("geneLowCoefOfVarFilter", {
  lowCVFiltered <- geneLowCoefOfVarFilter(t(testdata100ME4[, -ncol(testdata100ME4)]))
  expect_equal(nrow(lowCVFiltered$fdata), 98)
})

test_that("geneLowValFilter", {
  lowValFiltered <- geneLowValueFilter(t(testdata100ME4[, -ncol(testdata100ME4)]))
  expect_equal(nrow(lowValFiltered$fdata), 100)
})

test_that("geneLowVarFilter", {
  lowVarFiltered <- geneLowVarianceFilter(t(testdata100ME4[, -ncol(testdata100ME4)]))
  expect_equal(nrow(lowVarFiltered$fdata), 90)
})

test_that("lookupGenesFromEnsemblIds", {
  ensemblIds <- c("ENSG00000000003", "ENSG00000000005")
  geneNames <- lookupGenesFromEnsemblIds(ensemblIds)
  expect_equal(geneNames$hgnc_symbol, c("TSPAN6", "TNMD"))
})

test_that("scaleAB adjusts a vector to the specified scale", {
  expect_equal(scaleAB(seq(from = 0, to = 10), 0, 1), 
               seq(from = 0, to = 1, by = 0.1))
})

test_that("sumOfPowers computes the power series of a matrix", {
  A <- matrix(abs(rnorm(10 * 10)), nrow = 10, ncol = 10)
  g <- A + A %^% 2 + A %^% 3 + A %^% 4
  expect_equal(sumOfPowers(A, 4), g)
})