Nothing
context("PomaLasso")
test_that("PomaLasso works", {
data("st000336")
normalized <- st000336 %>%
POMA::PomaImpute(method = "knn") %>%
POMA::PomaNorm(method = "log_scaling")
normalized_test <- normalized
normalized_test_less <- normalized
Biobase::pData(normalized_test)$Group <- c(rep("C", 30), rep("G", 20), rep("P", 7))
Biobase::pData(normalized_test_less)$Group <- "Control"
lasso_res <- PomaLasso(normalized, alpha = 1, ntest = NULL, nfolds = 3, labels = TRUE)
ridge_res <- PomaLasso(normalized, alpha = 0, ntest = NULL, nfolds = 10)
enet_res <- PomaLasso(normalized, alpha = 0.5, ntest = NULL, nfolds = 5, labels = TRUE)
lasso_self_lambda <- PomaLasso(normalized, alpha = 1, ntest = NULL, nfolds = 10, lambda = seq(0.002, 20, length.out = 100))
## TABLES
expect_false(nrow(lasso_res$coefficients) == nrow(ridge_res$coefficients))
expect_false(nrow(lasso_res$coefficients) == nrow(enet_res$coefficients))
expect_equal(ncol(lasso_res$coefficients), ncol(ridge_res$coefficients))
expect_equal(ncol(ridge_res$coefficients), ncol(enet_res$coefficients))
expect_equal(ncol(lasso_res$coefficients), ncol(lasso_self_lambda$coefficients))
## PLOTS
df_a <- layer_data(lasso_res$coefficientPlot)
df_b <- layer_data(ridge_res$coefficientPlot)
df_e <- layer_data(enet_res$coefficientPlot)
df_c <- layer_data(lasso_res$cvLassoPlot)
df_d <- layer_data(ridge_res$cvLassoPlot)
expect_false(length(df_a$y) == length(df_b$y))
expect_false(length(df_c$y) == length(df_d$y))
expect_false(length(df_a$y) == length(df_e$y))
## ERRORS
expect_error(PomaLasso(normalized, alpha = 2))
expect_error(PomaLasso(normalized, alpha = -0.5))
expect_error(PomaLasso(iris, alpha = 1))
expect_error(PomaLasso(normalized_test, alpha = 1))
expect_error(PomaLasso(normalized_test_less, alpha = 1))
expect_error(PomaLasso())
expect_error(PomaLasso(normalized, ntest = 60))
expect_error(PomaLasso(normalized, ntest = 2))
})
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