tests/testthat/test_filterNA.R

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

context("filterNA method")

test_that("filterNA for matrix", {
    M <- matrix(rnorm(20, 1), 5, 4)
    M[2, 1] <- NA
    M[3, 1:2] <- NA
    M[4, 1:3] <- NA
    M[5, ] <- NA
    rownames(M) <- LETTERS[1:5]
    expect_equal(rownames(filterNA(M, 0/4)), LETTERS[1])
    expect_equal(rownames(filterNA(M, 1/4)), LETTERS[1:2])
    expect_equal(rownames(filterNA(M, 2/4)), LETTERS[1:3])
    expect_equal(rownames(filterNA(M, 3/4)), LETTERS[1:4])
    expect_equal(rownames(filterNA(M, 4/4)), LETTERS[1:5])
    M[1, 1] <- NA
    expect_equal(dim(filterNA(M, 0/4)), c(0, 4))
})

test_that("filterNA for MSnSet", {
    data(msnset, package = "MSnbase")
    exprs(msnset)[sample(prod(dim(msnset)), 120)] <- NA
    msnset2 <- filterNA(msnset, 1/4)
    expect_true(nrow(msnset) > nrow(msnset2))
})

test_that("filterNA with pattern", {
    M <- matrix(rnorm(40), ncol = 4)
    rownames(M) <- 1:10
    M[1:5, 1] <- NA
    M[c(1, 3, 5), 4] <- NA
    M[c(1, 5, 10), 2] <- NA
    res <- filterNA(M, pattern = "0110")
    expect_equal(rownames(res), as.character(c(2, 3, 4, 6, 7, 8, 9)))
    res <- filterNA(M, pattern = "0111")
    expect_equal(rownames(res), as.character(c(2, 4, 6, 7, 8, 9)))
    res0 <- filterNA(M, pattern = "1111")
    res1 <- filterNA(M, pNA = 0)
    expect_identical(res0, res1)
})

test_that("filterZero", {
    data(naset, package = "MSnbase")
    zeroset <- naset
    exprs(zeroset)[is.na(naset)] <- 0
    nares <- filterNA(naset)
    zerores <- filterZero(zeroset)
    nares@processingData@processing <-
        zerores@processingData@processing
    exprs(zerores)[exprs(zerores) == 0] <- NA
    expect_equal(nares, zerores)
})

test_that("filterZero with pNA", {
    data(naset, package = "MSnbase")
    zeroset <- naset
    exprs(zeroset)[is.na(naset)] <- 0
    nares <- filterNA(naset, pNA = 0.5)
    zerores <- filterZero(zeroset, pNA = 0.5)
    nares@processingData@processing <-
        zerores@processingData@processing
    exprs(zerores)[exprs(zerores) == 0] <- NA
    expect_equal(nares, zerores)
})