tests/testthat/test_geseca.R

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

context("Gene Set Co-Regulation Analysis")

test_that("GESECA: is reproducible", {
    data("exampleExpressionMatrix")
    data("examplePathways")

    set.seed(1)
    gr1 <- geseca(pathways=examplePathways, E=exampleExpressionMatrix)

    set.seed(1)
    gr2 <- geseca(pathways=examplePathways, E=exampleExpressionMatrix)

    expect_equal(gr1$pval, gr2$pval)
})


test_that("GESECA: works with zero pathways", {
    data("exampleExpressionMatrix")
    data("examplePathways")
    set.seed(42)
    sampleSize <- 11

    gr1 <- geseca(pathways=examplePathways, E=exampleExpressionMatrix,
                  sampleSize=sampleSize, minSize=50, maxSize=10)
    expect_equal(nrow(gr1), 0)

    gr2 <- geseca(pathways=examplePathways[5],
                  E=exampleRanks, sampleSize=sampleSize, minSize=5)

    expect_equal(colnames(gr2), colnames(gr1))
})


test_that("GESECA: works with pathways of one gene", {
    data("exampleExpressionMatrix")
    data("examplePathways")
    set.seed(42)
    sampleSize <- 11

    p <- rownames(exampleExpressionMatrix)[1]
    gr1 <- geseca(pathways=list(p=p), E=exampleExpressionMatrix,
                  sampleSize=sampleSize, minSize=1, maxSize=10)
    expect_equal(nrow(gr1), 1)

    pl <- plotCoregulationProfile(p, E=exampleExpressionMatrix)


})

test_that("GESECA checks gene names", {
    data("exampleExpressionMatrix")
    data("examplePathways")
    E <- exampleExpressionMatrix
    rownames(E)[1] <- rownames(E)[2]

    expect_error(geseca(E=E, pathways=examplePathways, minSize=15))

    E <- exampleExpressionMatrix
    rownames(E)[1] <- NA
    expect_error(geseca(E=E, pathways=examplePathways, minSize=15))

    E <- unname(exampleExpressionMatrix)
    expect_error(geseca(E=E, pathways=examplePathways, minSize=15))
})


test_that("GESECA: The eps parameter works correctly", {
    data("exampleExpressionMatrix")
    data("examplePathways")

    set.seed(42)
    expect_warning(gr <- geseca(E=exampleExpressionMatrix, pathways=examplePathways, eps=1e-10))

    expect_true(all(gr$pval >= 1e-10))
    expect_true(any(is.na(gr$log2err)))
})



test_that("GESECA: throws a warning when sampleSize is less than 3", {
    data("exampleExpressionMatrix")
    data("examplePathways")

    set.seed(42)
    expect_silent(geseca(pathways   = examplePathways,
                         E          = exampleExpressionMatrix,
                         sampleSize = 5,
                         eps        = 0.0))
    expect_warning(geseca(pathways   = examplePathways,
                          E          = exampleExpressionMatrix,
                          sampleSize = 1,
                          eps        = 0.0))

})

test_that("GESECA: throws a warning when reaching eps", {
    data("exampleExpressionMatrix")
    data("examplePathways")

    set.seed(42)
    expect_warning(gr <- geseca(E=exampleExpressionMatrix, pathways=examplePathways, eps=1e-10))
})