Nothing
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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