Feature/r6 class

.gitignore

@@ -52,3 +52,7 @@ rsconnect/
 *.o
 *.so
 .DS_Store
+
+# pkgdown site (deployed to gh-pages)
+docs/*
+!docs/.nojekyll

DESCRIPTION

@@ -1,28 +1,24 @@
 Package: splikit
-Title: A toolkit for analysing RNA splicing in scRNA-seq data
-Version: 1.0.6
-Authors@R: 
+Title: A Toolkit for Analysing RNA Splicing in scRNA-Seq Data
+Version: 2.0.0
+Authors@R:
     person("Arsham", "Mikaeili Namini", , "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9453-6951"))
-Description: 
-  Splikit /ˈsplaɪ.kɪt/ is a toolkit designed for the analysis of high-dimensional single-cell 
-  splicing data. It provides a framework to extract and work with ratio-based data structures 
-  derived from single-cell RNA sequencing experiments. The package avoids the need for bulky 
-  S4 objects by offering direct and efficient manipulation of matrices. Core functionalities 
-  are implemented in C++ via Rcpp to ensure high performance and scalability on large datasets.
-URL: https://arshammik.github.io/splikit/, https://github.com/Arshammik/splikit
-BugReports: https://github.com/Arshammik/splikit/issues
+Description: A toolkit designed for the analysis of high-dimensional single-cell
+    splicing data. Provides a framework to extract and work with ratio-based
+    data structures derived from single-cell RNA sequencing experiments.
+    Offers both a modern R6 object-oriented interface and direct matrix
+    manipulation functions. Core functionalities are implemented in C++ via
+    'Rcpp' to ensure high performance and scalability on large datasets.
+URL: https://csglab.github.io/splikit/, https://github.com/csglab/splikit
+BugReports: https://github.com/csglab/splikit/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-Imports: Matrix, data.table, methods, stats, Rcpp, RcppArmadillo
+RoxygenNote: 7.3.3
+Imports: Matrix, data.table, methods, stats, Rcpp, R6
 LinkingTo: Rcpp, RcppArmadillo
-Suggests: testthat (>= 3.0.0)
+Suggests: testthat (>= 3.0.0), knitr, rmarkdown
 Config/testthat/edition: 3
-NeedsCompilation: yes
-Packaged: 2025-05-09 22:41:00 UTC; arsham79
-Author: Arsham Mikaeili Namini [aut, cre]
-    (<https://orcid.org/0000-0002-9453-6951>)
-Maintainer: Arsham Mikaeili Namini <arsham.mikaeilinamini@mail.mcgill.ca>
-Depends: R (>= 3.5.0)
+VignetteBuilder: knitr
+Depends: R (>= 4.1.0)

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(SplikitObject)
 export(find_variable_events)
 export(find_variable_genes)
 export(get_pseudo_correlation)
@@ -13,6 +14,7 @@ export(make_junction_ab)
 export(make_m1)
 export(make_m2)
 export(make_velo_count)
+export(splikit)
 import(Matrix)
 import(Rcpp)
 import(data.table)
@@ -21,8 +23,11 @@ importClassesFrom(Matrix,dgTMatrix)
 importClassesFrom(Matrix,dsCMatrix)
 importClassesFrom(Matrix,dsTMatrix)
 importFrom(Matrix,Matrix)
+importFrom(Matrix,nnzero)
 importFrom(Matrix,readMM)
+importFrom(Matrix,rowSums)
 importFrom(Matrix,sparseMatrix)
+importFrom(R6,R6Class)
 importFrom(Rcpp,evalCpp)
 importFrom(data.table,":=")
 importFrom(data.table,.GRP)
@@ -34,4 +39,7 @@ importFrom(data.table,fread)
 importFrom(data.table,is.data.table)
 importFrom(data.table,setDT)
 importFrom(data.table,setnames)
+importFrom(methods,as)
+importFrom(stats,na.omit)
+importFrom(stats,setNames)
 useDynLib(splikit, .registration = TRUE)

R/RcppExports.R

@@ -37,6 +37,40 @@ standardizeSparse_variance_vst <- function(matSEXP, display_progress = FALSE) {
     .Call(`_splikit_standardizeSparse_variance_vst`, matSEXP, display_progress)
 }
 
+#' Memory-efficient M2 computation building CSC format directly
+#'
+#' 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
+#'
+#' Memory usage: O(nnz_output) + O(n_groups) workspace
+#' vs previous: O(n_groups * n_cells) + O(6 * nnz_output)
+#'
+#' @param M1 Sparse matrix (dgCMatrix) of inclusion counts (events x cells)
+#' @param group_ids Integer vector of group IDs for each event
+#' @param n_threads Number of threads for OpenMP (default 1)
+#'
+#' @return Sparse matrix M2 with same dimensions as M1
+#'
+#' @keywords internal
+make_m2_cpp_parallel <- function(M1, group_ids, n_threads = 1L) {
+    .Call(`_splikit_make_m2_cpp_parallel`, M1, group_ids, n_threads)
+}
+
+#' Legacy function - redirects to memory-efficient version
+#'
+#' @param M1 Sparse matrix (dgCMatrix) of inclusion counts (events x cells)
+#' @param group_ids Integer vector of group IDs for each event
+#' @param n_threads Number of threads for OpenMP (default 1)
+#'
+#' @return Sparse matrix M2 with same dimensions as M1
+#'
+#' @keywords internal
+make_m2_cpp <- function(M1, group_ids, n_threads = 1L) {
+    .Call(`_splikit_make_m2_cpp`, M1, group_ids, n_threads)
+}
+
 rowVariance_cpp <- function(mat) {
     .Call(`_splikit_rowVariance_cpp`, mat)
 }