make_m2_cpp_parallel: Memory-efficient M2 computation building CSC format directly

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

Memory-efficient M2 computation building CSC format directly

Description

This version minimizes memory usage by:

• Building CSC format directly (no triplet intermediate)

• Using O(n_groups) workspace per column instead of dense group_sums matrix

• Two-pass algorithm: count then fill

Usage

make_m2_cpp_parallel(M1, group_ids, n_threads = 1L)

Arguments

M1	Sparse matrix (dgCMatrix) of inclusion counts (events x cells)
group_ids	Integer vector of group IDs for each event
n_threads	Number of threads for OpenMP (default 1)

Details

Memory usage: O(nnz_output) + O(n_groups) workspace vs previous: O(n_groups * n_cells) + O(6 * nnz_output)

Value

Sparse matrix M2 with same dimensions as M1

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