VISTA S4 Class Definition

The VISTA class extends SummarizedExperiment. All analysis metadata (DE results, summaries, cutoffs, grouping info, etc.) is stored in the metadata() slot of the object.

Details

Core elements stored in metadata(v):

• $de_results: named SimpleList of DE result tables.

• $de_summary: named SimpleList of DEG summary tables.

• $de_cutoffs: named list of thresholds (log2FC, p-value type/cutoff, method settings).

• $group: list with column, palette, colors describing the grouping/fill scheme.

• $provenance: list with constructor version, timestamp, session info.

• $vista_schema_version: metadata schema tag used for compatibility checks.

Feature-level annotations live in rowData(v), sample metadata in colData(v), and normalized counts (and any additional assays) in assay(v, "norm_counts") by default. Use create_vista() as the primary end-user constructor. Advanced users can convert an existing SummarizedExperiment with as_vista().

See also

create_vista, as_vista, validate_vista