make_m1: make_m1

In splikit: Analysing RNA Splicing in Single-Cell RNA Sequencing Data

make_m1

Description

This function processes junction abundance data from multiple samples to create a splicing modality inclusion matrix (M1). It merges event data, handles start and end coordinate groups, ensures matrix compatibility, and includes robust error handling.

Usage

make_m1(junction_ab_object, min_counts = 1, verbose = FALSE)

Arguments

junction_ab_object	A named list where each element represents a sample's junction abundance data. Each element must contain eventdata and a sparse matrix.
min_counts	Numeric (default 1). Minimum count threshold for filtering events. Events with total counts below this threshold will be removed.
verbose	Logical (default FALSE). If TRUE, prints detailed progress messages during processing.

Details

The function requires the following libraries: data.table, and Matrix.

Value

A list containing the processed data from all samples:

m1_inclusion_matrix

A matrix representing the processed inclusion values for all events across all samples.

event_data

A data.table containing the merged and grouped metadata for each event.

Examples

# Example usage
junction_abundance_object <- load_toy_SJ_object()
result <- make_m1(junction_abundance_object)
m1_matrix <- result$m1_inclusion_matrix
event_metadata <- result$event_data

splikit documentation built on May 13, 2026, 9:08 a.m.