inst/scripts/test-data.R

In MahShaaban/curatedAdipoArray: A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations

testthat::context('test clean data')

library(testthat)
library(tidyverse)
library(Biobase)
library(org.Mm.eg.db)

test_that("clean data is formated properly.", {
    symbols <- keys(org.Mm.eg.db, 'SYMBOL')

    fls <- list.files(
      'cleandata',
      full.names = TRUE
    )

    esets <- map(fls, read_rds)

    expect_true(all(unlist(map(esets, ~is(.x, 'ExpressionSet')))))
    expect_true(all(unlist(map(esets, ~nrow(pData(.x)) > 1))))
    expect_true(all(unlist(map(esets, ~ncol(pData(.x)) > 1))))
    expect_true(all(unlist(map(esets, ~ncol(exprs(.x)) > 1))))
    expect_true(all(unlist(map(esets, ~ncol(exprs(.x)) > 1))))
    expect_true(all(unlist(map(esets, ~length(intersect(rownames(.x), symbols)) > 100))))

})

test_that('combined data is formated properly.', {
    symbols <- keys(org.Mm.eg.db, 'SYMBOL')
    md <- read_tsv('inst/extdata/curated_metadata.tsv')

    eset <- read_rds('cleandata/genetic_perturbation.rds')

    expect_true(all(rownames(eset) %in% symbols))
    expect_true(all(colnames(eset) %in% md$sample_id))

    eset <- read_rds('cleandata/pharmacological_perturbation.rds')

    expect_true(all(rownames(eset) %in% symbols))
    expect_true(all(colnames(eset) %in% md$sample_id))
})