tests/testthat/test-cis-grubbs.R

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

withr::local_options(list(ISAnalytics.verbose = FALSE))
agg <- aggregate_values_by_key(integration_matrices, association_file,
    value_cols = c("seqCount", "fragmentEstimate")
)

#------------------------------------------------------------------------------#
# Test CIS_grubbs
#------------------------------------------------------------------------------#
test_that("CIS_grubbs produces correct df", {
    output_cols <- c(
        "GeneName", "GeneStrand", "chr", "n_IS_perGene",
        "min_bp_integration_locus", "max_bp_integration_locus",
        "IS_span_bp", "avg_bp_integration_locus",
        "median_bp_integration_locus", "distinct_orientations",
        "n", "mean", "sd",
        "median", "trimmed", "mad",
        "min", "max", "range",
        "skew", "kurtosis",
        "average_TxLen",
        "raw_gene_integration_frequency",
        "integration_frequency_withtolerance",
        "minus_log2_integration_freq_withtolerance",
        "zscore_minus_log2_int_freq_tolerance",
        "neg_zscore_minus_log2_int_freq_tolerance", "t_z_mlif",
        "tdist2t", "tdist_pt", "tdist_bonferroni_default",
        "tdist_bonferroni", "tdist_fdr", "tdist_benjamini",
        "tdist_positive_and_corrected", "tdist_positive",
        "tdist_positive_and_correctedEM"
    )
    result <- CIS_grubbs(agg)
    expect_true(ncol(result$cis) == 37 & nrow(result$cis) == 501)
    expect_true(all(output_cols %in% colnames(result$cis)))
    expect_equal(nrow(result$missing_genes), 5)
    ## -- Group
    result <- CIS_grubbs(agg, by = "SubjectID")
    expect_true(is.list(result$cis) & length(result$cis) == 2)
    expect_true(nrow(result$cis$PT001) == 250 & ncol(result$cis$PT001) == 37)
    expect_true(nrow(result$cis$PT002) == 292 & ncol(result$cis$PT002) == 37)
    expect_equal(nrow(result$missing_genes), 5)

    result <- CIS_grubbs(agg, by = "SubjectID", results_as_list = FALSE)
    expect_true(ncol(result$cis) == 38 & nrow(result$cis) == 542)
    expect_true("group" %in% colnames(result$cis))
    expect_equal(nrow(result$missing_genes), 5)
})

test_that("CIS_grubbs errors for char non-standard refgene", {
    expect_error(
        {
            result <- CIS_grubbs(agg, genomic_annotation_file = "my_file.tsv")
        },
        class = "genomic_file_char"
    )
})

test_that("CIS_grubbs warns missing genes if verbose", {
    withr::local_options(list(ISAnalytics.verbose = TRUE))
    expect_warning(
        {
            result <- CIS_grubbs(agg)
        },
        class = "warn_miss_genes"
    )
})

#------------------------------------------------------------------------------#
# Test CIS_grubbs_overtime
#------------------------------------------------------------------------------#
test_that("CIS_grubbs_overtime fails if group missing", {
    expect_error({
        CIS_grubbs_overtime(agg, group = c("A", "B"))
    })
})

test_that("CIS_grubbs_overtime fails if as_df incorrect", {
    expect_error({
        CIS_grubbs_overtime(agg, as_df = "first")
    })
})

test_that("CIS_grubbs_overtime returns correctly nested list", {
    cis_ov <- CIS_grubbs_overtime(agg, as_df = FALSE)
    expect_true(is.list(cis_ov) & all(names(cis_ov) == c(
        "missing_genes",
        "missing_is", "cis"
    )))
    expect_true(all(names(cis_ov$cis) == c("PT001", "PT002")))
    expect_true(all(names(cis_ov$cis$PT001) == c(
        "0030", "0060", "0090",
        "0180", "0360"
    )))
    expect_true(all(names(cis_ov$cis$PT002) == c(
        "0030", "0060", "0090",
        "0180", "0360"
    )))
    expect_equal(nrow(cis_ov$missing_genes), 5)
    expect_equal(cis_ov$missing_is$absolute, 25)
})

test_that("CIS_grubbs_overtime returns correctly list one level", {
    cis_ov <- CIS_grubbs_overtime(agg, as_df = "group")
    expect_true(is.list(cis_ov) & all(names(cis_ov) == c(
        "missing_genes",
        "missing_is", "cis"
    )))
    expect_true(all(names(cis_ov$cis) == c("PT001", "PT002")))
    expect_true(is.data.frame(cis_ov$cis$PT001) & is.data.frame(cis_ov$cis$PT002))
    expect_true("TimePoint" %in% colnames(cis_ov$cis$PT001) &
        "TimePoint" %in% colnames(cis_ov$cis$PT002))
    expect_true(all(c(
        "0030", "0060", "0090",
        "0180", "0360"
    ) %in% cis_ov$cis$PT001$TimePoint))
    expect_true(all(c(
        "0030", "0060", "0090",
        "0180", "0360"
    ) %in% cis_ov$cis$PT002$TimePoint))
    expect_equal(nrow(cis_ov$missing_genes), 5)
    expect_equal(cis_ov$missing_is$absolute, 25)
})

test_that("CIS_grubbs_overtime returns correctly single df", {
    cis_ov <- CIS_grubbs_overtime(agg, as_df = TRUE)
    expect_true(is.list(cis_ov) & all(names(cis_ov) == c(
        "missing_genes",
        "missing_is", "cis"
    )))
    expect_true(is.data.frame(cis_ov$cis))
    expect_true("TimePoint" %in% colnames(cis_ov$cis))
    expect_true("group" %in% colnames(cis_ov$cis))
    expect_true(all(c(
        "0030", "0060", "0090",
        "0180", "0360"
    ) %in% cis_ov$cis$TimePoint))
    expect_true(all(c("PT001", "PT002") %in% cis_ov$cis$group))
    expect_equal(nrow(cis_ov$missing_genes), 5)
    expect_equal(cis_ov$missing_is$absolute, 25)
})