tests/testthat/test_scudoTest.R

In Matteo-Ciciani/scudo: Signature-based Clustering for Diagnostic Purposes

context("Test scudoTest")
library(rScudo)

test_that("scudoTest selects right features", {

    # Scudo Result for training
    exprData <- data.frame(a = 11:20,
                           b = 16:25,
                           c = rev(1:10),
                           d = c(1:2, rev(3:10)))
    rownames(exprData) <- letters[11:20]
    grps <- as.factor(c("G1", "G1", "G2", "G2"))
    nTop <- 2
    nBottom <- 3
    p <- 0.05

    res <- .performScudo(exprData, grps, nTop, nBottom, NULL, FALSE, FALSE)

    #Examples of scudoTest
    testExpData <- data.frame(e = 11:20,
                              f = 16:25,
                              g = rev(1:10),
                              h = c(1:2, rev(3:10)))
    rownames(testExpData) <- letters[11:20]
    grps1 <- as.factor(c("G1", "G2", "G2", "G1"))
    grps2 <- as.factor(c("G1", "G2", "G3", "G1"))
    grps3 <- NULL

    # Testing ScudoRes obj produced
    expect_s4_class(scudoTest(res, testExpData, grps1, 1, 3), "ScudoResults")

    # test for null groups
    expect_s4_class(scudoTest(res, testExpData, grps3, 1, 3), "ScudoResults")

    # tests on warnings and errors

    expect_message(scudoTest(res, testExpData, grps2, 1, 3))

    rownames(testExpData) <- letters[1:10]
    expect_error(suppressWarnings(scudoTest(res, testExpData, grps1, 1, 3)))

})