tests/testthat/test_group_standards.R

In rformassspectrometry/MetaboAnnotation: Utilities for Annotation of Metabolomics Data

#' define some variable for test 
x <- data.frame(
    row.names = c("Malic Acid", "Pyridoxic Acid", "Thiamine", "Uric acid",
                "dUTP", "N-Formyl-L-methionine"),
    "adduct_1" = c(135.0288, 184.0604, 265.1118, 169.0356, 468.9809, 178.0532),
    "adduct_2" = c(157.0107, 206.0424, 287.0937, 191.0176, 490.9628, 200.0352)
)
x <- as.matrix(x)

#' Expected list to get for maximum of 3 standard per group 
results <- list(c("Malic Acid", "Pyridoxic Acid", "Thiamine"), 
                c("Uric acid", "dUTP", "N-Formyl-L-methionine"))

test_that("essentially that .iterative_grouping works", {
    expect_equal(.iterative_grouping(x, max_nstd = 3, min_diff = 2), results)
    expect_is(.iterative_grouping(x, max_nstd = 3, min_diff = 2), "list")
})


#' test for randomization
set.seed(123) 
#' Create a matrix with compound names and ion masses
x <- matrix(c(349.0544, 371.0363, 325.0431, 347.0251, 581.0416, 603.0235,
              167.0564, 189.0383, 150.0583, 172.0403, 171.0053, 192.9872,
              130.0863, 152.0682, 768.1225, 790.1044),
            ncol = 2, byrow = TRUE)

rownames(x) <- c("IMP", "UMP", "UDP-glucuronate", "1-Methylxanthine",
                 "Methionine", "Dihydroxyacetone phosphate", "Pipecolic acid",
                 "CoA")
colnames(x) <- c("[M+H]+", "[M+Na]+")

#' run using `.iterative_grouping`
standard_groups <- .iterative_grouping(x, max_nstd = 4, min_diff = 2)

#' run using `.random_grouping`.
standard_groups_r <- .randomize_grouping(x, max_nstd = 4,
                                         min_nstd = 3,
                                         min_diff = 2)
min_nstd <- 3
test_that("randomization improves results", {
    expect_true(length(standard_groups) > length(standard_groups_r))
    expect_true(any(lengths(standard_groups_r) > min_nstd))
    expect_false(length(standard_groups_r) == 0 )
})

#check format of global function ouput
global_result <- createStandardMixes(x, max_nstd = 4,
                                     min_nstd = 3,
                                     min_diff = 2, iterativeRandomizati = TRUE)
test_that("out put format is right", {
    expect_true(is.data.frame(global_result))
    expect_equal(ncol(x)+1 , ncol(global_result))
    expect_equal(nrow(x), nrow(global_result))
})