tests/testthat/test_score_delta.R

In hclimente/scudo: Switch Catcher, Uprooting Differentially-expressed Ones

expression <- read.table(text = "
                         transcript sample tpmCtrl tpmCase
                         A1 s1 1 1
                         A2 s1 1 1
                         A3 s1 1 1
                         A1 s2 3 NA
                         A2 s2 2 NA
                         A3 s2 1 NA
                         A1 s3 NA 1
                         A2 s3 NA 2
                         A3 s3 NA 3
                         A1 s4 3 1
                         A2 s4 2 2
                         A3 s4 1 3
                         ", header = TRUE, stringsAsFactors = FALSE)
tx2gene <- read.table(text = "
                      transcript gene
                      A1 A
                      A2 A
                      A3 A
                      B1 B
                      ", header = TRUE, stringsAsFactors = FALSE)

dPSI <- calculate_dPSI(expression, tx2gene)
pdPSI <- score_delta(dPSI, transcript, psiCtrl, dPSI, minSamples = 2)

test_that('output is as expected', {

    expect_true(is.data.frame(pdPSI))
    expect_equal(ncol(pdPSI), 9)

})

test_that('dPSI p-value calculation is correct', {

    for (tx in c('A1','A2','A3')) {
        f <- compute_ecdf(subset(dPSI, transcript == tx)$psiCtrl, 0, 2)
        expect_equal(subset(pdPSI, transcript == tx)$p,
                     f(subset(pdPSI, transcript == tx)$dPSI))
    }

})