The MolecularAssay - Class

A class to represent molecular assay data, including analysis results, metrics, and statistical summaries. The MolecularAssay class encapsulates various components of assay data including raw and processed metrics, analytical results, and associated metadata like the assay name and molecular type.

(In further documentation the shorter term assay is used to refer to molecular assays.)

Slots

active_mtr

Character string indicating which matrix to extract and use by default.

analysis

List of analysis results where each element can represent a different analysis aspect such as DEA or CNV.

meta_var

Data.frame of meta data for the variables of this assay - the molecules.

mtr_counts

Matrix object storing raw counts from the assay. Rownames should corresponds to the molecule names. Colnames should correspond to the barcodes (IDs) of the observations to which the molecule counts were mapped.

mtr_proc

List of processed data matrices.

modality

Character value. A string that best characterizes the type of molecular data the assay carries (e.g., "gene", "protein"). More on molecular modalities in SPATA2 can be found here.

signatures

Named list of character vectors.

Molecular signatures are sets of molecules (such as genes or proteins) that are associated with specific biological states, processes, or conditions. This slot stores the molecular signatures detected in the assay data. Each signature is represented as a vector of molecule names in a named list, where the names of the list slots correspond to the signature. Read more on molecular signatures here.