tests/testthat/test-estimate.R

In MSstatsPTM: Statistical Characterization of Post-translational Modifications

test_that("PTMestimate() takes and returns the right format", {
    s <- PTMsimulateExperiment(
        nGroup=2, nRep=2, nProtein=1, nSite=2, nFeature=5,
        logAbundance=list(
            PTM=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05),
            PROTEIN=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05)
        )
    )
    est <- PTMestimate(PTMnormalize(s))

    expect_output(str(est), "List of 2")
    expect_identical(names(est), c("PTM", "PROTEIN"))

    expect_output(str(est[["PTM"]]), "List of 4")
    expect_output(str(est[["PROTEIN"]]), "List of 3")

    expect_identical(names(est[["PTM"]]), c("protein", "site", "param", "df"))
    expect_identical(names(est[["PROTEIN"]]), c("protein", "param", "df"))

    s[["PROTEIN"]] <- NULL
    est <- PTMestimate(PTMnormalize(s))

    expect_output(str(est), "List of 1")
    expect_identical(names(est), "PTM")
})