tests/testthat/test-validate_pairs.R

In alexvpickering/rkal: Run, Import, and Export 'kallisto' Quantifications

context("select pairs validation")

test_that("validate_pairs requires two rows to be paired", {

    # single row fails
    rows <- 1
    pairs <- rep(NA, 4)
    reps <- rep(NA, 4)
    expect_match(validate_pairs(pairs, rows, reps), 'at least two rows')

    # using two rows works
    rows2 <- c(1, 2)
    expect_null(validate_pairs(pairs, rows2, reps))
})

test_that("validate_pairs requires two non-replicate rows to be paired", {
    rows <- c(1, 2)
    pairs <- rep(NA, 4)
    reps <- c(1, 1, 2, 2)

    expect_match(validate_pairs(pairs, rows, reps), 'at least two non-replicate rows')

    rows2 <- c(1, 2, 3, 4)
    expect_null(validate_pairs(pairs, rows2, reps))
})

test_that("validate_pairs doesn't allow a replicate not included in a pair", {
    rows <- c(1, 3)
    pairs <- rep(NA, 4)
    reps <- c(1, 1, 2, 2)

    expect_match(validate_pairs(pairs, rows, reps), 'All replicates must be included in the same pair')

    rows2 <- c(1, 2, 3, 4)
    expect_null(validate_pairs(pairs, rows2, reps))
})

test_that("validate_pairs requires exactly two unique replicates, or one replicate and 1 additional sample", {
    rows <- c(1, 2, 3, 4, 5)
    pairs <- rep(NA, 6)
    reps <- c(1, 1, 2, 2, NA, NA)

    expect_match(validate_pairs(pairs, rows, reps), 'exactly two replicate groups')

    rows2 <- c(1, 2, 3, 4)
    expect_null(validate_pairs(pairs, rows2, reps))
})

test_that("validate_pairs doesn't allow overwriting of existing pairs", {
    rows <- c(1, 2, 3, 4)
    reps <- rep(NA, 6)
    pairs <- c(1, 1, NA, NA, 2, 2)

    expect_match(validate_pairs(pairs, rows, reps), 'already belong to a pair')

    rows2 <- c(3, 4)
    expect_null(validate_pairs(pairs, rows2, reps))
})