Create a MatisseObject

The single constructor for MatisseObject. Combines a Seurat object with isoform-resolved splicing data. The operating mode is detected automatically from the inputs you supply:

Usage

CreateMatisseObject(
  seurat,
  junction_counts = NULL,
  transcript_counts = NULL,
  ioe_files = NULL,
  event_data = NULL,
  junction_data = NULL,
  min_coverage = 5L,
  verbose = TRUE
)

Arguments

seurat

A Seurat object. Required.

junction_counts

A sparse matrix (dgCMatrix, cells x junctions) of raw per-junction read counts. Row names must match colnames(seurat). Triggers junction mode. Default: NULL.

transcript_counts

A matrix or sparse matrix (transcripts x cells) of raw transcript-level counts. Stored as Assay5("transcript") in the Seurat object. Column names must overlap with colnames(seurat). Default: NULL.

ioe_files

Character vector of paths to SUPPA2 .ioe files. When supplied together with transcript_counts, triggers event mode and PSI is computed at construction. Default: NULL.

event_data

A data.frame defining splice events (junction mode only). Required columns: event_id, gene_id, chr, strand, event_type, inclusion_junctions, exclusion_junctions. Default: NULL.

junction_data

A data.frame of junction annotations. Required columns: junction_id, chr, start, end, strand, gene_id. Default: NULL.

min_coverage

Integer. Minimum total transcript counts per cell per event to report a PSI value (event mode only). Default: 5.

verbose

Logical. Print construction progress. Default: TRUE.

Value

A MatisseObject.

Details

• Junction mode (short-read): pass junction_counts. Junction counts are stored as Assay5("junction") inside the Seurat object. Call CalculatePSI afterwards to compute PSI values.

• Event mode (long-read): pass transcript_counts and ioe_files. Transcript counts are stored as Assay5("transcript") and PSI is computed immediately from the supplied SUPPA2 .ioe event definitions, stored as Assay5("psi").

You can also pass transcript_counts alone (without ioe_files) to store the transcript assay without computing PSI – for example, when you want to run SCTransform on transcript-level counts and compute PSI separately.

Examples

if (FALSE) { # \dontrun{
library(Seurat)
counts <- matrix(rpois(200, 5), nrow = 20,
                 dimnames = list(paste0("Gene", 1:20),
                                 paste0("Cell", 1:10)))
seu <- CreateSeuratObject(counts)

# Junction mode
jxn <- make_junction_counts()
obj <- CreateMatisseObject(seurat = seu, junction_counts = jxn)

# Event mode
tx  <- make_transcript_counts()
obj <- CreateMatisseObject(seurat = seu, transcript_counts = tx,
                           ioe_files = "path/to/events.ioe")
} # }