The MatisseObject S4 class

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 operating modes are supported, set automatically at construction:

"junction"

Short-read mode. Raw junction counts are stored as Assay5("junction") (junctions × cells). PSI is computed later by CalculatePSI and stored as Assay5("psi").

"event"

Long-read mode. Transcript counts (e.g. from Bagpiper or FLAMES) are stored as Assay5("transcript"). PSI is computed at construction time from SUPPA2 .ioe event definitions and stored as Assay5("psi").

Functions

• show(MatisseObject): Display a summary of a MatisseObject.

• x[[i: Access cell metadata or Seurat slots via [[. Checks seurat@meta.data first; falls back to the embedded Seurat object (assays, reductions, etc.).

Slots

seurat

A Seurat object. Contains all per-cell data: gene expression, splice assays ("junction", "transcript", "psi"), cell metadata (QC metrics, cluster labels), and dimensionality reductions.

event_data

A data.frame with one row per splice event. Required columns: event_id, gene_id, chr, strand, event_type, inclusion_junctions, exclusion_junctions.

junction_data

A data.frame with one row per junction. Required columns: junction_id, chr, start, end, strand, gene_id.

mode

Character. "junction" for short-read objects; "event" for long-read objects.

version

Character string recording the Matisse version used to create the object.

misc

Named list for user-defined extra data.