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VISTA S4 Class Definition

VISTA-class.Rd

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

Value

A VISTA S4 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

Examples

methods::showClass('VISTA')
#> Class "VISTA" [package "VISTA"]
#> 
#> Slots:
#>                                                                               
#> Name:            colData            assays             NAMES   elementMetadata
#> Class:         DataFrame    Assays_OR_NULL character_OR_NULL         DataFrame
#>                         
#> Name:           metadata
#> Class:              list
#> 
#> Extends: 
#> Class "SummarizedExperiment", directly
#> Class "RectangularData", by class "SummarizedExperiment", distance 2
#> Class "Vector", by class "SummarizedExperiment", distance 2
#> Class "Annotated", by class "SummarizedExperiment", distance 3
#> Class "vector_OR_Vector", by class "SummarizedExperiment", distance 3