ReducedExperiment

ReducedExperiment provides SummarizedExperiment-like containers for storing and manipulating dimensionally-reduced assay data.

Key Features:

• Dual dataset manipulation: The ReducedExperiment classes allow users to simultaneously manipulate their original dataset and their decomposed data.
• Method-specific output storage: Stores additional method-specific outputs such as feature loadings alongside reduced data representations.
• Stabilised independent component analysis (sICA) support: Implements utilities and specialised classes for the application of sICA.
• Weighted gene correlation network analysis (WGCNA) support: Implements utilities and specialised classes for the application of WGCNA.

Scientific Applications:

• Dimensionality reduction in -omics data: Enables storage and manipulation of dimensionally-reduced representations of high-dimensional assay data.
• Independent component analysis: Supports stabilised ICA for decomposing -omics datasets into independent components with associated feature loadings.
• Gene correlation network analysis: Supports WGCNA for identifying modules of correlated features in -omics data.

Methodology:

ReducedExperiment implements SummarizedExperiment-like container classes that store original assay data alongside decomposed data and method-specific outputs such as feature loadings. The package provides specialised classes and utilities for stabilised independent component analysis (sICA) and weighted gene correlation network analysis (WGCNA).