The MatisseObject S4 class — MatisseObject-class • Matisse

The central data structure for Matisse. It wraps a Seurat object and adds isoform-resolved splicing layers. All per-cell data – junction counts, PSI values, transcript counts, and QC metrics – live inside the embedded Seurat object as named assays (Assay5) or cell metadata (meta.data). Nothing is duplicated outside the Seurat object.

Usage

# S4 method for class 'MatisseObject'
show(object)

# S4 method for class 'MatisseObject'
dim(x)

# S4 method for class 'MatisseObject,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

# S4 method for class 'MatisseObject,ANY,ANY'
x[[i, j, ...]]

# S4 method for class 'MatisseObject'
x$name

Arguments

object: A MatisseObject.
x: A MatisseObject.
i: Cell barcodes (character) or integer indices.
j: Event IDs (character) or integer indices.
...: Ignored.
drop: Ignored.
name: Metadata column name or Seurat/Signac function name.

Details

Two input modes are supported, set automatically at construction:

"junction": Short-read mode. Raw junction counts (from STARsolo) are stored as Assay5("isoform") (junctions x cells). Call CalculatePSI to compute PSI values.
"transcript": Long-read mode. Transcript isoform counts (from Bagpiper, FLAMES, or LIQA) are stored as Assay5("isoform") (transcripts x cells). Call CalculatePSI to compute PSI values.

After CalculatePSI, PSI values are stored as Assay5("psi") (splice events x cells).

Functions

show(MatisseObject): Display a summary of a MatisseObject.
x[[i: Access cell metadata or Seurat slots via [[. Returns metadata columns as bare vectors (matching Matisse convention), then falls back to the embedded Seurat object's [[ for assays, reductions, etc. The explicit metadata check is load-bearing — Seurat's own [[ returns metadata columns wrapped in a 1-column data.frame.

Slots

seurat: A Seurat object. Contains all per-cell data: gene expression, splice assays ("isoform", "psi"), cell metadata (QC metrics, cluster labels), and dimensionality reductions.
input.mode: Character. "junction" for short-read (STARsolo junction counts) objects; "transcript" for long-read (Bagpiper / FLAMES / LIQA transcript counts) objects.
version: Character string recording the Matisse version used to create the object.
misc: Named list for user-defined extra data.