@@ -495,7 +495,22 @@ setMethod(

       z = as.integer(res$z),

       pseudocount = 1e-20

     )

-    estRmat[seq(nrow(counts)), which(batch == bat)] <- estRmat.temp

+    

+    # Speed up sparse matrix value assignment by cbind -> order recovery

+    

+    allCol <- paste0("col_", 1:ncol(estRmat))

+    colnames(estRmat) <- allCol

+    

+    subCol <- paste0("col_", which(batch == bat))

+    colnames(estRmat.temp) <- subCol

+    

+    estRmat <- estRmat[, !(allCol %in% subCol)]

+    estRmat <- cbind(estRmat, estRmat.temp)

+    

+    # Recover order

+    estRmat <- estRmat[, allCol]

+    

+    #(Old method) estRmat[seq(nrow(counts)), which(batch == bat)] <- estRmat.temp

     dimnames(estRmat) <- list(geneNames, allCellNames)

     resBatch[[bat]] <- list(

@@ -6,6 +6,11 @@

 using namespace Rcpp;

+#ifdef RCPP_USE_GLOBAL_ROSTREAM

+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();

+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();

+#endif

+

 // decontXEM

 Rcpp::List decontXEM(const Eigen::MappedSparseMatrix<double>& counts, const NumericVector& counts_colsums, const NumericVector& theta, const bool& estimate_eta, const NumericMatrix& eta, const NumericMatrix& phi, const IntegerVector& z, const bool& estimate_delta, const NumericVector& delta, const double& pseudocount);

 RcppExport SEXP _celda_decontXEM(SEXP countsSEXP, SEXP counts_colsumsSEXP, SEXP thetaSEXP, SEXP estimate_etaSEXP, SEXP etaSEXP, SEXP phiSEXP, SEXP zSEXP, SEXP estimate_deltaSEXP, SEXP deltaSEXP, SEXP pseudocountSEXP) {