tests/testthat/test_statistical_tests.R

In dcanr: Differential co-expression/association network analysis

library(dcanr)
library(Biobase)
library(edgeR)
library(SummarizedExperiment)

context('Statistical tests ')

#data to test methods
set.seed(360)
x <- matrix(rnorm(40), 4, 10)
colnames(x) = 1:ncol(x)
rownames(x) = 1:nrow(x)
cond <- rep(1:2, each = ncol(x) / 2)

#pick a representative set - exclude any method that uses perm test during check
getInfMethods <- function() {
  infmethods = c('zscore', 'diffcoex', 'ebcoexpress')
  if (!require('EBcoexpress')) {
    infmethods = setdiff(infmethods, 'ebcoexpress')
  }
  if (!require('COSINE')) {
    infmethods = setdiff(infmethods, 'ecf')
  }
  if (!require('GeneNet')) {
    infmethods = setdiff(infmethods, 'ggm-based')
  }

  return(infmethods)
}

scorelist <- lapply(getInfMethods(), function (m) dcScore(x, cond, m))
names(scorelist) <- getInfMethods()

test_that('Testing calls work', {
  for (m in getInfMethods()) {
    expect_is(dcTest(scorelist[[!!m]], x, cond), 'matrix')
  }
})

#generate test matrices
testmats <- lapply(scorelist, function(s) dcTest(s, x, cond))

test_that('Correct dimensions of results', {
  for (m in getInfMethods()) {
    expect_equal(dim(testmats[[!!m]]), c(4, 4))
  }
})

test_that('Attributes attached to results', {
  for (m in getInfMethods()) {
    expect_output(str(attr(testmats[[!!m]], 'dc.test')), regexp = '.')
  }
})

test_that('Diagonals are NAs', {
  for (m in getInfMethods()) {
    expect_equal(sum(is.na(diag(testmats[[!!m]]))), nrow(x))
  }
})

test_that('Values are in range for statistical tests', {
  for (m in setdiff(getInfMethods(), 'diffcoex')) {
    expect_gte(min(testmats[[!!m]], na.rm = TRUE), 0)
    expect_lte(max(testmats[[!!m]], na.rm = TRUE), 1)
  }
})