Abstract intermediate class for SE-backed datasets

ExploreDatasetSE holds the SummarizedExperiment backend reference and implements the accessor contract uniformly for every SE shape. Concrete subclasses (ExploreDatasetSE_RNASeq, _CountQC, _CrisprCountQC, _Proteomics) override two private methods only:

• .build_config(se) — returns the per-instance config list at $initialize() time

• .prep() — populates private$.features_df, private$.de_dfs, private$.fid_lookup from the SE

This class is not instantiable on its own — instantiate a concrete subclass instead.

Value

An R6 class generator; the concrete subclasses' $new() returns an object inheriting from ExploreDatasetSE.

Super class

ExploreDataset -> ExploreDatasetSE

Methods

Public methods

• ExploreDatasetSE$new()

• ExploreDatasetSE$backend()

• ExploreDatasetSE$backend_kind()

• ExploreDatasetSE$samples()

• ExploreDatasetSE$features()

• ExploreDatasetSE$de()

• ExploreDatasetSE$assay_names()

• ExploreDatasetSE$assay()

• ExploreDatasetSE$enrichment()

• ExploreDatasetSE$enrichment_input()

• ExploreDatasetSE$clone()

Inherited methods

• ExploreDataset$all_pathways()
• ExploreDataset$assay_label()
• ExploreDataset$background_expression()
• ExploreDataset$contrast_label()
• ExploreDataset$contrast_meta()
• ExploreDataset$contrasts()
• ExploreDataset$data_type()
• ExploreDataset$de_all()
• ExploreDataset$de_display_extras()
• ExploreDataset$enrichment_filter()
• ExploreDataset$enrichment_kinds()
• ExploreDataset$enrichment_table()
• ExploreDataset$factor_levels()
• ExploreDataset$factor_names()
• ExploreDataset$feature_display()
• ExploreDataset$feature_id_kind()
• ExploreDataset$feature_ids()
• ExploreDataset$format()
• ExploreDataset$has_assay()
• ExploreDataset$has_de()
• ExploreDataset$has_enrichment()
• ExploreDataset$has_pvalue()
• ExploreDataset$n_features()
• ExploreDataset$n_samples()
• ExploreDataset$omics_class()
• ExploreDataset$organism()
• ExploreDataset$primary_assay()
• ExploreDataset$primary_assay_name()
• ExploreDataset$primary_contrast()
• ExploreDataset$primary_grouping()
• ExploreDataset$proteomics_choices()
• ExploreDataset$raw_assay()
• ExploreDataset$raw_assay_name()
• ExploreDataset$ref_build()
• ExploreDataset$sample_factor()
• ExploreDataset$sample_ids()
• ExploreDataset$secondary_grouping()
• ExploreDataset$sgrna_to_gene()
• ExploreDataset$source()

---

ExploreDatasetSE$new()

Wrap a SummarizedExperiment: store it, build the config from it, and prepare the feature and DE tables.

Usage

ExploreDatasetSE$new(se)

Arguments

se

A SummarizedExperiment.

---

ExploreDatasetSE$backend()

The wrapped SummarizedExperiment.

Usage

ExploreDatasetSE$backend()

---

ExploreDatasetSE$backend_kind()

Returns "se".

Usage

ExploreDatasetSE$backend_kind()

---

ExploreDatasetSE$samples()

Sample metadata from colData(), with the SUSHI [Factor] suffix stripped from column names, rownames set to sample IDs, and a Name column added.

Usage

ExploreDatasetSE$samples()

---

ExploreDatasetSE$features()

Feature annotation table, prepared from rowData() by the subclass.

Usage

ExploreDatasetSE$features()

---

ExploreDatasetSE$de()

DE table of one contrast, prepared from rowData() by the subclass; an empty data.frame when none was prepared. Errors on an unknown contrast.

Usage

ExploreDatasetSE$de(contrast)

Arguments

contrast

Contrast name, one of contrasts().

---

ExploreDatasetSE$assay_names()

Canonical assay names from the config's assay map whose SE assay exists; computed assays are always included.

Usage

ExploreDatasetSE$assay_names()

---

ExploreDatasetSE$assay()

One assay as a features x samples matrix with rows renamed to feature IDs; normalised_log2, vst, fpkm and tpm are computed when the config maps them to no SE assay.

Usage

ExploreDatasetSE$assay(name, features = NULL, samples = NULL)

Arguments

name

Canonical assay name, one of assay_names().

features

Feature IDs (rows) to keep; NULL keeps all.

samples

Sample IDs (columns) to keep; NULL keeps all.

---

ExploreDatasetSE$enrichment()

Enrichment results of one kind, read from metadata(se) and flattened to a named list; an empty list when absent. contrast is not used.

Usage

ExploreDatasetSE$enrichment(contrast, kind)

Arguments

contrast

Contrast name; not used by this backend.

kind

"ora" or "gsea".

---

ExploreDatasetSE$enrichment_input()

Enrichment inputs read from metadata(se)$enrichInput, with NULL fields and no selections when absent. contrast is not used.

Usage

ExploreDatasetSE$enrichment_input(contrast)

Arguments

contrast

Contrast name; not used by this backend.

---

ExploreDatasetSE$clone()

The objects of this class are cloneable with this method.

Usage

ExploreDatasetSE$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

se <- readRDS(system.file("examples/proteomics/SummarizedExperiment.rds", package = "exploreDE"))
eds <- new_explore_dataset(se)
inherits(eds, "ExploreDatasetSE")
#> [1] TRUE
eds$assay_names()
#> [1] "intensities"
dim(eds$raw_assay())
#> [1] 1384    6