tests/testthat/test-PomaUnivariate.R

context("PomaUnivariate")

test_that("PomaUnivariate works", {

  data("st000284")
  data("st000336")

  st000336 <- POMA::PomaImpute(st000336, method = "knn")
  
  dims_for_ttest_and_mann <- c(ncol(t(Biobase::exprs(st000336))), 6)
  dims_for_aov <- c(ncol(t(Biobase::exprs(st000284))), length(levels(as.factor(Biobase::pData(st000284)[,1]))) + 2)
  dims_for_krusk <- c(ncol(t(Biobase::exprs(st000284))), length(levels(as.factor(Biobase::pData(st000284)[,1]))) + 3)
  
  univ_ttest <- PomaUnivariate(st000336, method = "ttest", adjust = "fdr")
  univ_aov <- PomaUnivariate(st000284, covariates = FALSE, method = "anova", adjust = "fdr")
  univ_aov_cov <- PomaUnivariate(st000284, covariates = TRUE, method = "anova", adjust = "fdr")
  univ_aov_cov2 <- PomaUnivariate(st000284, covariates = TRUE, method = "anova", adjust = "bonferroni")

  univ_mann <- PomaUnivariate(st000336, method = "mann", adjust = "fdr")
  univ_kruskal <- PomaUnivariate(st000284, method = "kruskal", adjust = "fdr")
  univ_kruskal2 <- PomaUnivariate(st000284, method = "kruskal", adjust = "BY")

  one_cov1 <- PomaUnivariate(st000336, covariates = FALSE, method = "anova", adjust = "fdr")
  one_cov2 <- PomaUnivariate(st000336, covariates = TRUE, method = "anova", adjust = "fdr")
  
  ##

  expect_equal(dims_for_ttest_and_mann, dim(univ_ttest))
  expect_equal(dims_for_aov, dim(univ_aov_cov))
  expect_equal(dims_for_aov, dim(univ_aov_cov2))
  expect_equal(dims_for_aov, dim(univ_aov))
  expect_false(all(univ_aov_cov == univ_aov_cov2))

  ##

  expect_equal(dims_for_ttest_and_mann, dim(univ_mann))
  expect_equal(dim(univ_kruskal), dim(univ_kruskal2))
  expect_false(all(univ_kruskal == univ_kruskal2))
  expect_equal(dims_for_krusk, dim(univ_kruskal))
  expect_equal(dims_for_krusk, dim(univ_kruskal2))
  
  expect_equal(dim(one_cov1), dim(one_cov2))
  expect_false(all(one_cov1$pvalue == one_cov2$pvalue))
  
  ##
  
  expect_error(PomaUnivariate(st000284, covariates = TRUE, method = "anov", adjust = "fdr"))
  expect_error(PomaUnivariate(st000284, covariates = TRUE, adjust = "fdr"))
  
  expect_error(PomaUnivariate(st000336, method = "ttest", adjust = "fd"))
  
  Biobase::pData(st000284) <- Biobase::pData(st000284)[1]
  expect_error(PomaUnivariate(st000284, method = "anova", covariates = TRUE, adjust = "fdr"))
  
  ##
  
  expect_error(PomaUnivariate(method = "ttest"))
  expect_error(PomaUnivariate(iris, method = "ttest"))
  
})

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POMA documentation built on Nov. 8, 2020, 6:26 p.m.