tests/testthat/test_convertCounts.R

In DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit

context("DGEobj.utils - tests for convertCounts.R functions")
skip_if(setup_failed)


test_that("convertCounts.R: convertCounts()", {
    # CPM
    ## Full Count Matrix "none" normalization
    count_matrix <- convertCounts(counts      = t_obj1$counts_orig,
                                  unit        = "CPM",
                                  log         = FALSE,
                                  normalize   = "none",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts_orig), dim(count_matrix))
    ## Full Count Matrix missing normalization
    count_matrix <- convertCounts(counts      = t_obj1$counts_orig,
                                  unit        = "CPM",
                                  normalize = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts_orig), dim(count_matrix))
    ## Full Count Matrix "true" normalization, testing backward compatibility
    count_matrix <- convertCounts(counts      = t_obj1$counts_orig,
                                  unit        = "CPM",
                                  log         = FALSE,
                                  normalize   = TRUE,
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts_orig), dim(count_matrix))
    expect_error(convertCounts(unit = "CPM"),
                 msg = "argument \"counts\" is missing, with no default")
    expect_error(convertCounts(counts = t_obj1$counts_orig),
                 msg = "argument \"unit\" is missing, with no default")
    ## Full Count Matrix "TMM" normalization
    count_matrix <- convertCounts(counts      = t_obj1$counts_orig,
                                  unit        = "CPM",
                                  log         = FALSE,
                                  normalize   = "TMM",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts_orig), dim(count_matrix))
    ## Full Count Matrix "RLE" normalization
    count_matrix <- convertCounts(counts      = t_obj1$counts_orig,
                                  unit        = "CPM",
                                  log         = TRUE,
                                  normalize   = "RLE",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts_orig), dim(count_matrix))
    ## Subset of the Count Matrix
    count_matrix <- convertCounts(counts = t_obj1$counts_orig[1:100, ], unit = "CPM")
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts[1:100,]), dim(count_matrix))

    # TPM
    ## Full Count Matrix normalize "none"
    genelength <- getItem(t_obj1, "geneData")$ExonLength
    ### FALSE log
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "TPM",
                                  geneLength  = genelength ,
                                  log         = FALSE,
                                  normalize   = "none",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    ### TRUE log
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "TPM",
                                  geneLength  = genelength ,
                                  log         = TRUE,
                                  normalize   = "none",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    ## testing genelength as a matrix
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "TPM",
                                  geneLength  = as.matrix(genelength) ,
                                  log         = FALSE,
                                  normalize   = "none",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    expect_error(convertCounts(counts = t_obj1$counts, unit = "TPM"), regexp = "geneLength is required for unit = FPK|FPKM|TPM")
    ## Full Count Matrix normalize "TMM"
    expect_warning(convertCounts(counts = t_obj1$counts,
                                 unit = "TPM",
                                 geneLength = genelength,
                                 normalize = "TMM"),
                   regexp = "TPM normalization overides TMM normalization!")
    ## Full Count Matrix normalize "upperquartile"
    expect_warning(convertCounts(counts = t_obj1$counts,
                                 unit = "TPM",
                                 geneLength = genelength,
                                 normalize = "upperquartile"),
                   regexp = "TPM normalization overides upperquartile normalization!")
    ## Full Count Matrix normalize "TMMWZP"
    expect_warning(convertCounts(counts = t_obj1$counts,
                                 unit = "TPM",
                                 geneLength = genelength,
                                 normalize = "TMMWZP"),
                   regexp = "TPM normalization overides TMMwzp normalization!")
    ## Full Count Matrix normalize "RLE"
    expect_warning(convertCounts(counts = t_obj1$counts,
                                 unit = "TPM",
                                 geneLength = genelength,
                                 normalize = "RLE"),
                   regexp = "TPM normalization overides RLE normalization!")
    expect_warning(convertCounts(counts = t_obj1$counts,
                                 unit = "TPM",
                                 geneLength = genelength,
                                 prior.count = 1,
                                 log = TRUE),
                   regexp = "Using a prior.count for logTPM calculations is not recommended and may produce unpredictable results!")
    ## Subset of the Count Matrix
    count_matrix <- convertCounts(counts = t_obj1$counts_orig[1:100, ],
                                  unit = "TPM",
                                  geneLength  = genelength[1:100])
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts[1:100,]), dim(count_matrix))

    # FPK
    ## Full Count Matrix normalize "none"
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "FPK",
                                  geneLength  = genelength ,
                                  log         = FALSE,
                                  normalize   = "none",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    ## Full Count Matrix normalize "none" with 0 genelength
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "FPK",
                                  geneLength  = integer(length(genelength)) ,
                                  log         = FALSE,
                                  normalize   = "none",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    ## Full Count Matrix normalize "TMM" with 0 genelength
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "FPK",
                                  geneLength  = integer(length(genelength)) ,
                                  log         = FALSE,
                                  normalize   = "TMM",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    ## Full Count Matrix normalize "TMM" log enabled
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "FPK",
                                  geneLength  = genelength,
                                  log         = TRUE,
                                  normalize   = "TMM",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    expect_error(convertCounts(counts = t_obj1$counts, unit = "FPK"), regexp = "geneLength is required for unit = FPK|FPKM|TPM")
    ## Full Count Matrix normalize "TMM" log disabled
    count_matrix <- convertCounts(counts = t_obj1$counts,
                                 unit = "FPK",
                                 geneLength = genelength,
                                 normalize = "TMM")
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    ## Full Count Matrix normalize "RLE"
    count_matrix <- convertCounts(counts = t_obj1$counts,
                                 unit = "FPK",
                                 geneLength = genelength,
                                 normalize = "RLE")
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))

    # FPKM
    ## Full Count Matrix normalize "none"
    count_matrix <- convertCounts(counts      = t_obj1$counts,
                                  unit        = "FPKM",
                                  geneLength  = genelength ,
                                  log         = FALSE,
                                  normalize   = "none",
                                  prior.count = NULL)
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    expect_error(convertCounts(counts = t_obj1$counts, unit = "FPKM"), regexp = "geneLength must be specified when unit is 'FPK', 'FPKM', or 'TPM.'")
    ## Full Count Matrix normalize "TMM"
    count_matrix <- convertCounts(counts = t_obj1$counts,
                                  unit = "FPKM",
                                  geneLength = genelength,
                                  normalize = "TMM")
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))
    ## Full Count Matrix normalize "RLE"
    count_matrix <- convertCounts(counts = t_obj1$counts,
                                  unit = "FPKM",
                                  geneLength = genelength,
                                  normalize = "RLE")
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts), dim(count_matrix))

    # Subset of the Count Matrix
    count_matrix <- convertCounts(counts = t_obj1$counts_orig[1:100, ],
                                  unit = "FPK",
                                  geneLength  = genelength[1:100])
    expect_true("matrix" %in% class(count_matrix))
    expect_identical(dim(t_obj1$counts[1:100,]), dim(count_matrix))
    # Testing assert
    ## countsMatrix
    msg  <-  "countsMatrix must be a numeric matrix or dataframe of N genes x M Samples. All columns must be numeric."
    expect_error(convertCounts(),
                 regexp = msg)
    expect_error(convertCounts(NULL),
                 regexp = msg)
    expect_error(convertCounts(data.frame()),
                 regexp = msg)
    expect_error(convertCounts(matrix()),
                 regexp = msg)
    expect_error(convertCounts(t_obj1$Sora_vs_BDL),
                 regexp = msg)
    expect_error(convertCounts(t_obj1$counts_orig %>% as.list()),
                 regexp = msg)
    ## unit
    msg <- "unit must be specified and must be one of 'CPM', 'FPKM', 'FPK' or 'TPM'."
    expect_error(convertCounts(counts = t_obj1$counts_orig),
                 regexp = msg)
    expect_error(convertCounts(counts = t_obj1$counts_orig,
                               unit = NULL),
                 regexp = msg)
    expect_error(convertCounts(counts = t_obj1$counts_orig,
                               unit = 123),
                 regexp = msg)
    expect_error(convertCounts(counts = t_obj1$counts_orig,
                               unit = c("CPM", "FPKM")),
                 regexp = msg)
    ## log
    msg <- "log must be a singular logical value. Assigning default value FALSE"
    expect_warning(convertCounts(counts      = t_obj1$counts_orig,
                                 unit        = "CPM",
                                 log         = NULL),
                   regexp = msg)
    expect_warning(convertCounts(counts      = t_obj1$counts_orig,
                                 unit        = "CPM",
                                 log         = "FALSE"),
                   regexp = msg)
    expect_warning(convertCounts(counts      = t_obj1$counts_orig,
                                 unit        = "CPM",
                                 log         = c(FALSE, FALSE)),
                   regexp = msg)
    ## normalize
    msg <- "normalize must be only one of the following values 'TMM', 'RLE', 'upperquartile', 'TMMwzp', 'none', TRUE, FALSE or NULL. Assigning default values 'none'"
    expect_warning(convertCounts(counts      = t_obj1$counts_orig,
                                 unit        = "CPM",
                                 normalize   = "NULL"),
                   regexp = msg)
    expect_warning(convertCounts(counts      = t_obj1$counts_orig,
                                 unit        = "CPM",
                                 normalize   = c(FALSE, TRUE)),
                   regexp = msg)
    expect_warning(convertCounts(counts      = t_obj1$counts_orig,
                                 unit        = "CPM",
                                 normalize   = c("TMM", "RLE")),
                   regexp = msg)
    expect_warning(convertCounts(counts      = t_obj1$counts_orig,
                                 unit        = "CPM",
                                 normalize   = 123),
                   regexp = msg)

})

test_that("convertCounts.R: tpm.on.subset()", {
    geneLength <- NULL
    if (attr(t_obj1, "source") == "Omicsoft") {
        geneLength <- getItem(t_obj1, "geneData")$ExonLength
    } else if ("effectiveLength_orig" %in% names(t_obj1)) {
        geneLength <- rowMeans(getItem(t_obj1, "effectiveLength_orig"), na.rm = TRUE)
    }

    # testing level gene
    tpmObj <- tpm.on.subset(t_obj1)
    expect_true("matrix" %in% class(tpmObj))
    # testing level isoform
    isoform_dgeObj <- t_obj1
    isoform_dgeObj <- addItem(dgeObj   = isoform_dgeObj,
                              item     = isoform_dgeObj$geneData_orig,
                              itemName = "isoformData_orig",
                              itemType = "meta")
    attr(isoform_dgeObj, "level") <- "isoform"
    tpmObj <- tpm.on.subset(isoform_dgeObj)
    expect_true("matrix" %in% class(tpmObj))

    ## dgeobj
    msg <- "dgeObj must be specified and should be of class 'DGEobj'."
    expect_error(tpm.on.subset("XYZ"), regexp = msg)
    expect_error(tpm.on.subset(), regexp = msg)
    expect_error(tpm.on.subset(NULL), regexp = msg)
    # testing level exon
    exon_dgeObj <- t_obj1
    attr(exon_dgeObj, "level") <- "exon"
    expect_error(tpm.on.subset(exon_dgeObj),
                 regexp = "The level of dgeObj should be of type 'isoform' or type 'gene'.")

    # testing for bad source attribute
    attr(isoform_dgeObj, "source") <- "XYZ"
    expect_error(tpm.on.subset(isoform_dgeObj),
                 regexp = "object 'geneLength' not found")
    # Testing assert
    ## applyFilter
    msg <- "applyFilter must be a singular logical value. Assigning default value TRUE."
    isoform_dgeObj <- t_obj1
    isoform_dgeObj <- addItem(dgeObj   = isoform_dgeObj,
                              item     = isoform_dgeObj$geneData_orig,
                              itemName = "isoformData_orig",
                              itemType = "meta")
    expect_warning(tpm.on.subset(isoform_dgeObj,
                                 applyFilter = NULL),
                   regexp = msg)
    expect_warning(tpm.on.subset(isoform_dgeObj,
                                 applyFilter = "FALSE"),
                   regexp = msg)
    expect_warning(tpm.on.subset(isoform_dgeObj,
                                 applyFilter = c(FALSE, FALSE)),
                   regexp = msg)
})

test_that("convertCounts.R: tpm.direct()", {
    genelength <- getItem(t_obj1, "geneData")$ExonLength
    tpmObj <- tpm.direct(t_obj1$counts, geneLength = genelength)
    expect_true("matrix" %in% class(tpmObj))

    # testing count as vector type
    tpmObj <- tpm.direct(counts = genelength, geneLength = genelength)
    expect_true("matrix" %in% class(tpmObj))

    # testing bad genelength parameter
    expect_error(tpm.direct(t_obj1$counts, geneLength = as.data.frame(genelength)),
                 regexp = "The dimensions of countsMatrix and geneLength should match.")

    # testing collapse parameter
    tpmObj <- tpm.direct(t_obj1$counts, geneLength = as.matrix(genelength), collapse = TRUE)
    expect_true("matrix" %in% class(tpmObj))

    #Testing assert
    ## countsMatrix
    msg  <-  "countsMatrix must be a numeric matrix of N genes x M Samples. All columns must be numeric."
    expect_error(tpm.direct(),
                 regexp = msg)
    expect_error(tpm.direct(NULL),
                 regexp = msg)
    expect_error(tpm.direct(data.frame()),
                 regexp = msg)
    expect_error(tpm.direct(matrix()),
                 regexp = msg)
    expect_error(tpm.direct(t_obj1$Sora_vs_BDL),
                 regexp = msg)
    expect_error(tpm.direct(t_obj1$counts_orig %>% as.list()),
                 regexp = msg)
    ## genelength
    expect_error(tpm.direct(t_obj1$counts), regexp = "geneLength must be specified")
    expect_error(tpm.direct(t_obj1$counts, geneLength = NULL), regexp = "geneLength must be specified")
    ## collapse
    genelength <- getItem(t_obj1, "geneData")$ExonLength
    tpmObj <- tpm.direct(t_obj1$counts, geneLength = genelength)
    msg <- "collapse must be a singular logical value. Assigning default value FALSE."
    expect_warning(tpm.direct(t_obj1$counts, geneLength = genelength,
                              collapse         = NULL),
                   regexp = msg)
    expect_warning(tpm.direct(t_obj1$counts, geneLength = genelength,
                              collapse         = "FALSE"),
                   regexp = msg)
    expect_warning(tpm.direct(t_obj1$counts, geneLength = genelength,
                              collapse         = c(FALSE, FALSE)),
                   regexp = msg)
})