Adding the modifications for version 1.0.4

.github/workflows/R-CMD-check.yml

@@ -12,14 +12,14 @@ jobs:
     strategy:
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.5' }
-          - { os: ubuntu-latest, r: '4.4' }
-          - { os: windows-latest, r: '4.5' }
-          - { os: windows-latest, r: '4.4' }
-          - { os: macos-latest, r: '4.5' }
-          - { os: macos-latest, r: '4.4' }
+          - { os: ubuntu-latest, r: 'release' }
+          - { os: ubuntu-latest, r: 'oldrel-1' }
+          - { os: windows-latest, r: 'release' }
+          - { os: windows-latest, r: 'oldrel-1' }
+          - { os: macos-latest, r: 'release' }
+          - { os: macos-latest, r: 'oldrel-1' }
     name: R ${{ matrix.config.r }} - ${{ matrix.config.os }}
-    
+
     steps:
       - uses: actions/checkout@v3
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: splikit
 Title: A toolkit for analysing RNA splicing in scRNA-seq data
-Version: 1.0.3
+Version: 1.0.4
 Authors@R: 
     person("Arsham", "Mikaeili Namini", , "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9453-6951"))
@@ -14,18 +14,14 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Imports: 
-  Matrix,
-  data.table,
-  methods,
-  stats,
-  Rcpp,
-  RcppArmadillo,
-  RcppEigen
-LinkingTo: 
-    Rcpp, 
-    RcppArmadillo,
-    RcppEigen
-Suggests: 
-    testthat (>= 3.0.0)
+Imports: Matrix, data.table, methods, stats, Rcpp, RcppArmadillo,
+        RcppEigen
+LinkingTo: Rcpp, RcppArmadillo, RcppEigen
+Suggests: testthat (>= 3.0.0)
 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)

R/feature_selection.R

@@ -2,9 +2,9 @@
 #'
 #' @param m1_matrix A matrix representing the inclusion matrix. Rows are events, columns are barcodes.
 #' @param m2_matrix A matrix representing the exclusion matrix. Rows are events, columns are barcodes.
+#' @param n_threads If the module OpenPM is available for your device, the function suggests using multi-thread processing for even faster computation.
 #' @param min_row_sum A numeric value specifying the minimum row sum threshold for filtering events. Defaults to 50.
 #' @param verbose Logical. If \code{TRUE} (default), prints progress and informational messages.
-#' @param n_threads If the module OpenPM is available for your device, the function suggests using multi-thread processing for even faster computation.
 #' @param ... Additional arguments to be passed.
 #'
 #' @return A \code{data.table} containing the events and their corresponding sum deviance values.
@@ -19,31 +19,16 @@
 #'  # printing the results
 #'  print(HVE[order(-sum_deviance)])
 #' @export
-find_variable_events <- function(m1_matrix, m2_matrix, min_row_sum = 50, verbose=TRUE, n_threads=1, ...) {
-
-  # Load necessary libraries
-  if (!requireNamespace("data.table", quietly = TRUE)) {
-    stop("The 'data.table' package is required but not installed.")
-  }
-
-  if (!requireNamespace("Rcpp", quietly = TRUE)) {
-    stop("The 'Rcpp' package is required but not installed.")
-  }
-
-  if (!requireNamespace("Matrix", quietly = TRUE)) {
-    stop("The 'Matrix' package is required but not installed.")
-  }
+find_variable_events <- function(m1_matrix, m2_matrix, min_row_sum = 50, n_threads=1, verbose=TRUE, ...) {
 
   # Check if matrices are sparse
   if (!(inherits(m1_matrix, "Matrix") && inherits(m2_matrix, "Matrix"))) {
     stop("Both 'm1_matrix' and 'm2_matrix' must be sparse matrices of class 'Matrix'.")
   }
-
   # Check matrix compatibility
   if (!identical(colnames(m1_matrix), colnames(m2_matrix))) {
     stop("The colnames (barcodes) of inclusion and exclusion matrices are not identical.")
   }
-
   if (!identical(rownames(m1_matrix), rownames(m2_matrix))) {
     stop("The rownames (junction events) of inclusion and exclusion matrices are not identical.")
   }
@@ -65,24 +50,26 @@ find_variable_events <- function(m1_matrix, m2_matrix, min_row_sum = 50, verbose
   sum_deviances <- numeric(nrow(m1_matrix))
   names(sum_deviances) <- rownames(m1_matrix)
 
-  for (lib in libraries) {
+  deviance_results <- lapply(libraries, function(lib) {
     filter <- which(meta[, ID] == lib)
     M1_sub <- m1_matrix[, filter, drop = FALSE]
     M2_sub <- m2_matrix[, filter, drop = FALSE]
 
-    # Calculate deviances using the C++ function
     deviance_values <- tryCatch({
       calcDeviances_ratio(M1_sub, M2_sub, n_threads)
     }, error = function(e) {
       stop("Error in calcDeviances_ratio function: ", e$message)
     })
-
     deviance_values <- c(deviance_values)
     names(deviance_values) <- rownames(M1_sub)
-    sum_deviances <- sum_deviances + deviance_values
-    if(verbose){cat("Calculating the deviances for sample", lib, "has been completed!\n")}
-  }
+    if(verbose) {
+      cat("Calculating the deviances for sample", lib, "has been completed!\n")
+    }
+    return(deviance_values)
+  })
 
+  # Combine all results
+  sum_deviances <- Reduce(`+`, deviance_results)
   rez <- data.table::data.table(events = names(sum_deviances), sum_deviance = as.numeric(sum_deviances))
   return(rez)
   cat("All Done!\n")
@@ -166,25 +153,38 @@ find_variable_genes <- function(gene_expression_matrix, method = "vst", ...) {
     sum_deviances <- numeric(nrow(gene_expression_matrix))
     names(sum_deviances) <- rownames(gene_expression_matrix)
 
-    # Loop over each library to compute deviances
-    for (lib in libraries) {
-      filter <- which(meta[, ID] == lib)
-      gene_expression_matrix_sub <- gene_expression_matrix[, filter, drop = FALSE]
-
-      # Calculate deviances using the C++ function
-      deviance_values <- tryCatch({
-        calcNBDeviancesWithThetaEstimation(as(gene_expression_matrix_sub, "dgCMatrix"))
-
-      }, error = function(e) {
-        stop("Error in calcNBDeviancesWithThetaEstimation function: ", e$message)
+    calculate_all_deviances <- function(gene_expression_matrix, meta, ID) {
+      # Get unique libraries
+      libraries <- unique(meta[, ID])
+
+      # Initialize results list
+      deviances_list <- vector("list", length(libraries))
+      names(deviances_list) <- libraries
+
+      # Getting the sim devinaces fir NB model
+      deviances_list <- lapply(libraries, function(lib) {
+        filter <- which(meta[, ID] == lib)
+        gene_expression_matrix_sub <- gene_expression_matrix[, filter, drop = FALSE]
+        deviance_values <- tryCatch({
+          calcNBDeviancesWithThetaEstimation(as(gene_expression_matrix_sub, "dgCMatrix"))
+        }, error = function(e) {
+          stop("Error in calcNBDeviancesWithThetaEstimation function: ", e$message)
+        })
+        deviance_values <- c(deviance_values)
+        names(deviance_values) <- rownames(gene_expression_matrix_sub)
+        cat("Calculating the deviances for sample", lib, "has been completed!\n")
+        return(deviance_values)
       })
 
-      deviance_values <- c(deviance_values)
-      names(deviance_values) <- rownames(gene_expression_matrix_sub)
-      sum_deviances <- sum_deviances + deviance_values
-      cat("Calculating the deviances for sample", lib, "has been completed!\n")
+      # Sum deviances across all libraries
+      sum_deviances <- Reduce(`+`, deviances_list)
+
+      return(sum_deviances)
     }
 
+    # Then use it:
+    sum_deviances <- calculate_all_deviances(gene_expression_matrix, meta, ID)
+
     # Compute row variance using the previously defined function
     row_var <- tryCatch({
       splikit::get_rowVar(M = gene_expression_matrix)

R/zzz.R

@@ -6,8 +6,8 @@
     "  at McGill University, Montreal. Distributed under the MIT License.\n",
     "  For documentation and examples, see the package vignette.\n",
     "-------------------------------------------------------------------------------------------------------\n",
-    "  Bienvenue dans Splikit — Développé par le Laboratoire de génomique computationnelle et statistique\n",
-    "  de l’Université McGill, à Montréal. Distribué sous licence MIT.\n",
+    "  Bienvenue dans Splikit — Developpe par le Laboratoire de genomique computationnelle et statistique\n",
+    "  de l’Universite McGill, a Montreal. Distribue sous licence MIT.\n",
     "  Pour la documentation et des exemples, consultez la vignette du package.\n",
     "=======================================================================================================\n"
   )

src/Makevars.linux

@@ -0,0 +1,4 @@
+## src/Makevars (Linux)
+CXX_STD = CXX14
+PKG_CXXFLAGS += -O3 -march=native -pipe -fopenmp
+PKG_LIBS += -fopenmp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)