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Runtime validator for a live ExploreDataset instance

Source: R/validate_explore_dataset.R
validate_explore_dataset.Rd

Checks subclass-agnostic invariants by walking the accessor API:

Usage

validate_explore_dataset(eds, strict = TRUE)

Arguments

eds

An ExploreDataset instance.

strict

If TRUE (default), stop() listing every failure. If FALSE, returns list(ok, errors) and never throws: a failing accessor is recorded as an error.

Value

Invisibly, TRUE on success (strict mode); or list(ok = logical(1), errors = character) (non-strict mode).

Details

  1. The runtime class is a concrete ExploreDataset subclass — not the abstract base or intermediate.

  2. Cross-references resolve: factor_names() are columns of samples(); every contrasts() entry has a working de() with the effect_log2fc and score_fdr columns; primary_grouping() is a member of factor_names(); primary_contrast() is in contrasts() (or NA).

  3. Assays: raw_assay_name() and primary_assay_name() are in assay_names(), and the raw assay's rownames / colnames agree with feature_ids() / sample_ids().

Cost is proportional to the number of contrasts (one de(c) round-trip each) plus a small constant of other accessor calls.

Examples

se <- readRDS(system.file("examples/proteomics/SummarizedExperiment.rds", package = "exploreDE"))
eds <- new_explore_dataset(se)
validate_explore_dataset(eds)
validate_explore_dataset(eds, strict = FALSE)
#> $ok
#> [1] TRUE
#> 
#> $errors
#> character(0)
#>