tests/testthat/test_Features.R

In QFeatures: Quantitative features for mass spectrometry data

data(feat1)

test_that("empty QFeatures", {
    feat0 <- QFeatures()
    expect_true(validObject(feat0))
    expect_true(isEmpty(feat0))
    expect_null(show(feat0))
})

test_that("Manual QFeatures", {
    ## code from inst/scripts/test_data.R
    ## used to generate feat1
    psms <- matrix(1:20, ncol = 2)
    colnames(psms) <- paste0("S", 1:2)
    rowdata <- DataFrame(Sequence = c("SYGFNAAR", "SYGFNAAR", "SYGFNAAR", "ELGNDAYK",
                                      "ELGNDAYK", "ELGNDAYK", "IAEESNFPFIK",
                                      "IAEESNFPFIK", "IAEESNFPFIK", "IAEESNFPFIK"),
                         Protein = c("ProtA", "ProtA", "ProtA", "ProtA", "ProtA",
                                     "ProtA", "ProtB", "ProtB", "ProtB", "ProtB"),
                         Var = 1:10)
    rownames(rowdata) <- rownames(psms) <- paste0("PSM", 1:10)
    coldata <- DataFrame(Group = 1:2)
    rownames(coldata) <- colnames(psms)
    psms <- SummarizedExperiment(psms, rowData = rowdata)
    feat2 <- QFeatures(list(psms = psms), colData = coldata)
    expect_true(validObject(feat2))
    ## subsetting
    expect_null(show(feat2))
    expect_equal(psms, feat2[[1]])
    expect_equal(psms, feat2[["psms"]])
    expect_equal(feat2, feat2[1:10, 1:2, 1])
    ## compare to serialised data
    ## data(feat1)
    ## expect_equivalent(feat1, feat2)
})


test_that("addAssay", {
    data(feat1)
    assay2 <- feat1[[1]]
    feat1 <- addAssay(feat1, assay2, name = "psms2")
    expect_identical(names(feat1), c("psms", "psms2"))
    expect_identical(feat1[[1]], feat1[[2]])
})

test_that("[,QFeatures", {
    data(feat1)
    feat1 <- aggregateFeatures(feat1, "psms", "Sequence", "peptides")
    expect_true(validObject(feat1[, , "psms"]))
    expect_true(validObject(feat1[, , "peptides"]))
    expect_true(validObject(feat1[, , 1]))
    expect_true(validObject(feat1[, , 2]))
})


test_that("RowData", {
    data(feat2)
    rd <- rowData(feat2)
    expect_identical(names(rd), paste0("assay", 1:3))
    expect_identical(rd[[1]], rowData(feat2[[1]]))
    expect_identical(rd[[2]], rowData(feat2[[2]]))
    expect_identical(rd[[3]], rowData(feat2[[3]]))
})


test_that("rowDataNames", {
    rdn <- rowDataNames(feat1)
    expect_identical(length(feat1), length(rdn))
    expect_identical(names(feat1), names(rdn))
    for (i in seq_along(length(feat1)))
        expect_identical(rdn[[i]], names(rowData(feat1[[i]])))
})


test_that("selectRowData", {
    x <- c("Sequence", "Protein")
    ft <- selectRowData(feat1, x)
    expect_identical(length(ft), length(feat1))
    expect_identical(names(ft), names(feat1))
    expect_identical(rowDataNames(ft)[[1]], x)
    expect_error(selectRowData(feat1))
    expect_message(ft <- selectRowData(feat1,
                                       c("Sequence", "Protein",
                                         "Var", "location", "pval",
                                         "var_not_found")))
    expect_identical(feat1, ft)
})



test_that("renaming", {
    data(feat1)
    feat1 <- aggregateFeatures(feat1, "psms", fcol = "Sequence",
                               name = "peptides", fun = colSums)
    feat1 <- aggregateFeatures(feat1, "peptides", fcol = "Protein",
                               name = "proteins", fun = colSums)
    expect_true(validObject(feat1))
    feat2 <- feat1
    names(feat2) <- LETTERS[1:3]
    expect_true(validObject(feat2))
    # Expect errors
    feat2@assayLinks[[1]]@name <- "foo"
    expect_error(validObject(feat2),
                 regexp = "@names not valid")
    feat2 <- feat1
    feat2@assayLinks[[1]]@from <- "bar"
    expect_error(validObject(feat2),
                 regexp = "@from not valid")
    expect_error(names(feat2) <- 1:3,
                 regexp = "must be a character")
    expect_error(names(feat2) <- letters[c(1,2,2)],
                 regexp = "is duplicated$")
})

test_that("assays must have unique rownames", {
    hlpsms <- hlpsms[1:10, ]
    ft1 <- readQFeatures(hlpsms, ecol = 1:10, name = "psms", fname = "Sequence")
    rownames(ft1[[1]][1:2]) <- rep("1", 2)
    expect_error(validObject(ft1))
})


test_that("longFormat", {
    colData(feat2)$X <- 1:12
    ## Select a single colDataCols and rowDataCols
    lt <- longFormat(feat2, rowDataCols = "Prot", colDataCols = "X")
    ## Check dimensions
    expect_equal(nrow(lt),
                 sum(apply(dims(feat2), 2, prod)))
    expect_identical(ncol(lt),
                     5L+2L)
    ## Check content
    expect_identical(lt$Prot,
                     unname(unlist(lapply(rowData(feat2), 
                                          ## Repeat 4x because 4 samples
                                          function(x) rep(x$Prot, 4)))))
    ## Select a single colDataCols and no rowDataCols (make sure that 
    ## the implementation does not break the MAE implementation)
    lt <- longFormat(feat2, colDataCols = "X")
    expect_equal(nrow(lt),
                 sum(apply(dims(feat2), 2, prod)))
    expect_identical(ncol(lt),
                     5L+1L)
    ## Select multiple rowDataCols
    lt <- longFormat(feat2, rowDataCols = c("Prot", "x"))
    expect_equal(nrow(lt),
                 sum(apply(dims(feat2), 2, prod)))
    expect_identical(ncol(lt),
                     5L+2L)
    ## Test error: rowDataCols is missing in rowData
    expect_error(longFormat(feat2, rowDataCols = "y"),
                 regexp = "not found")
})