tests/testthat/test_requantify.R

In synapter: Label-free data analysis pipeline for optimal identification and quantitation

context("requantify")

f <- data.frame(isotopicDistr.run1="1_0:1000;1_1:100;1_2:10;1_3:1;",
                isotopicDistr.run2="1_0:800;1_1:100;1_2:10;1_3:1;",
                isotopicDistr.run3="1_0:2000;1_1:200;1_2:20;1_3:2;",
                isotopicDistr.run4="1_0:6000;1_1:1000;1_2:100;1_3:10;1_4:1",
                stringsAsFactors=FALSE)

im <- matrix(c(1000, 100, 10, 1, NA,
               800, 100, 10, 1, NA,
               2000, 200, 20, 2, NA,
               6000, 1000, 100, 10, 1), nrow=4, ncol=5, byrow=TRUE,
               dimnames=list(paste("isotopicDistr", paste0("run", 1:4),
                                   sep="."),
                             c("1_0", "1_1", "1_2", "1_3", "1_4")))

test_that(".isUnsaturatedIsotope", {
    munsat <- im
    mode(munsat) <- "logical"
    munsat[] <- TRUE
    munsat[1:3, 5] <- NA
    msat <- munsat
    msat[3:4, 1] <- FALSE
    expect_equal(synapter:::.isUnsaturatedIsotope(im, Inf), munsat)
    expect_equal(synapter:::.isUnsaturatedIsotope(im, 1500), msat)
})

test_that(".runsUnsaturated", {
    iso <- c("1_0", "1_1", "1_2", "1_3", "1_4")
    expect_equal(synapter:::.runsUnsaturated(im, Inf),
                 setNames(rep(TRUE, 5), iso))
    expect_equal(synapter:::.runsUnsaturated(im, 1500),
                 setNames(rep(c(FALSE, TRUE), c(1, 4)), iso))
})

test_that(".isCommonIsotope", {
    expect_equal(synapter:::.isCommonIsotope(im),
                 setNames(rep(c(TRUE, FALSE), c(4, 1)),
                          c("1_0", "1_1", "1_2", "1_3", "1_4")))
    expect_equal(synapter:::.isCommonIsotope(im[-(1:4),]),
                 setNames(rep(FALSE, 5), colnames(im)))
})

test_that(".filterMissingRuns", {
    mmissing <- im
    mmissing[2,] <- NA
    expect_equal(synapter:::.filterMissingRuns(mmissing), im[-2,])
})

test_that(".names2chargesIsotopes", {
    expect_equal(synapter:::.names2chargesIsotopes(c("1_0", "1_1", "2_3")),
                 list(charges=c(1, 1, 2), isotopes=c(0, 1, 3)))
})

test_that(".referenceRun", {
    m <- matrix(c(100, NA, 100,
                  200, 200, 200,
                  1e3, 1e3, 1e3,
                  1e5, 200, 200,
                  0, 120, 0), nrow=5, byrow=TRUE)
    expect_identical(synapter:::.referenceRun(m, m <= 1e3), 3L)
})

test_that("requantifySum, all isotopes below threshold", {
  int <- setNames(c(1111, 911, 2222, 7111), colnames(f))
  sat5000_int <- setNames(c(111, 111, 222, 1111), colnames(f))

  expect_equal(synapter:::.requantifySum(im, Inf,
                                         onlyCommonIsotopes=FALSE),
               int)
  expect_equal(synapter:::.requantifySum(im, 5000,
                                         onlyCommonIsotopes=FALSE),
               sat5000_int)
})

test_that("requantifySum, only common isotopes", {
  int <- setNames(c(1111, 911, 2222, 7110), colnames(f))
  sat5000_int <- setNames(c(111, 111, 222, 1110), colnames(f))
  satNA5000_int <- setNames(c(111, NA_real_, 222, 1110), colnames(f))

  expect_equal(synapter:::.requantifySum(im, Inf,
                                         onlyCommonIsotopes=TRUE),
               int)
  expect_equal(synapter:::.requantifySum(im, 5000,
                                         onlyCommonIsotopes=TRUE),
               sat5000_int)
  NA5000 <- im
  NA5000[2,] <- NA
  expect_equal(synapter:::.requantifySum(NA5000, 5000,
                                         onlyCommonIsotopes=TRUE),
               satNA5000_int)
})

test_that("requantifyReferenceRun", {

  int <- setNames(c(1111, 911, 2222, 7111), colnames(f))
  sat5000_int <- setNames(c(1111, 911, 2222, 11111), colnames(f))

  expect_equal(synapter:::.requantifyReferenceRun(im, Inf), int)
  expect_equal(synapter:::.requantifyReferenceRun(im, 5000), sat5000_int)

  # nothing in common
  notCommon <- matrix(c(1000, 100, 10, NA, NA,
                        NA, NA, NA, 800, 100), byrow=TRUE, nrow=2, ncol=5,
                      dimnames=list(c("run1", "run2"),
                                    c("1_0", "1_1", "1_2", "2_0", "2_1")))
  expect_equal(synapter:::.requantifyReferenceRun(notCommon, Inf),
               setNames(c(1110, 900), c("run1", "run2")))
  ## nothing in common, that's why just the first run (the reference) is
  ## returned
  expect_equal(synapter:::.requantifyReferenceRun(notCommon, 100),
               setNames(c(1110, NA_real_), c("run1", "run2")))
})

test_that(".applyByChargeState", {
  m <- matrix(c(1000, 100, 10, NA, NA,
                10000, 1000, NA, 800, 100), byrow=TRUE, nrow=2, ncol=5,
                dimnames=list(c("run1", "run2"),
                              c("1_0", "1_1", "1_2", "2_0", "2_1")))
  r <- matrix(c(1110, 0, 11000, 900), byrow=TRUE, nrow=2, ncol=2,
                dimnames=list(c("run1", "run2"), c("1", "2")))
  expect_error(synapter:::.applyByChargeState(m, c(1, 1, 2, 2)))
  expect_equal(synapter:::.applyByChargeState(m, c(1, 1, 1, 2, 2),
                                              rowSums, na.rm=TRUE), r)
})