tests/testthat/test-summarizeMolecularProfiles.R

In bhklab/ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

library(testthat)
library(ToxicoGx)

## TODO:: Can probably rewrite this using an apply function?

context("Testing if summarizeMolecularProfiles error handling works correctly...")

# tSet
context("...Checking for correct tSet param errors...")
test_that("Errors if given more than one tSet as parameter.", {
    expect_error(
        summarizeMolecularProfiles(
            c(TGGATESsmall, TGGATESsmall), mDataType="rna",
            cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=fNames(TGGATESsmall,"rna"), duration="8",
            dose=c("Control", "High"), summary.stat="median",
            fill.missing=TRUE, verbose=TRUE
        ))
})

# mDataTypes
context("...Checking for correct mDataType param errors...")
test_that("Warning if given more than one mDataType.", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType=c("rna", "cnv"),
            cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=fNames(TGGATESsmall, "rna"), duration="8",
            dose=c("Control", "High"), summary.stat="median",
            fill.missing=FALSE, verbose=TRUE
        )
    )
})
test_that("Errors if given mDataType as type other than character.", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType=1, cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=fNames(TGGATESsmall,"rna"), duration="8",
            dose=c("Low", "Medium"), summary.stat="mean",
            fill.missing=FALSE, verbose=FALSE
        )
    )
})
test_that("Errors if specified mDataType is not in the tSet.", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="cnv", cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=fNames(TGGATESsmall,"rna"), duration="8",
            dose=c("Control", "High"), summary.stat="first",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})

# cell_lines
context("...Checking for correct cell_lines param errors...")
test_that("Errors if given cell_lines as type other than character.", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=5,
            drugs=head(treatmentNames(TGGATESsmall)),
            features=fNames(TGGATESsmall,"rna"), duration="8",
            dose=c("Control", "High"), summary.stat="last",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})
test_that("Errors if specified cell_lines are not in the tSet", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines='NOTINtSET',
            drugs=head(treatmentNames(TGGATESsmall)),
            features=fNames(TGGATESsmall,"rna"), duration="8",
            dose=c("Control", "High"), summary.stat="median",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})

# drugs
context("...Checking for correct drugs param errors...")
test_that("Errors if given drugs are type other than character.", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs=5, features=fNames(TGGATESsmall,"rna"), duration="8",
            dose=c("Control", "High"), summary.stat="mean",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})
test_that("Errors if specified drugs are not in the tSet.", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs="NOTINtSET", features=fNames(TGGATESsmall,"rna"),
            duration="8", dose=c("ontrol", "High"), summary.stat="first",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})

# features
context("...Checking for correct features param errors....")
test_that("Errors if given features as type other than character", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=c(5), duration="8",
            dose=c("Control", "High"), summary.stat="last",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})
test_that("Errors if given features as type other than character", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=c(5), duration="8",
            dose=c("Control", "High"), summary.stat="median",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})

# duration
context("...Checking for correct duration param errors")
test_that("Errors if given duration as type other than character", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=c(5), duration=8,
            dose=c("Control", "High"), summary.stat="mean",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})
test_that("Errors if given features as type other than character", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=c(5), duration="NOTINtSET",
            dose=c("Control", "High"), summary.stat="first",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})

# dose
context("...Checking for correct dose param errors")
test_that("Errors if given features as type other than character", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=c(5), duration="8",
            dose=c(1, 2), summary.stat="last",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})
test_that("Errors if specified doses are not in the tSet", {
    expect_error(
        summarizeMolecularProfiles(
            TGGATESsmall, mDataType="rna", cell_lines=sampleNames(TGGATESsmall),
            drugs=head(treatmentNames(TGGATESsmall)),
            features=c(5), duration="8",
            dose="NOTINTtSET", summary.stat="median",
            fill.missing=TRUE, verbose=TRUE
        )
    )
})