@@ -30,7 +30,7 @@ LinkingTo: Rcpp, RcppEigen

 License: MIT + file LICENSE

 Encoding: UTF-8

 LazyData: true

-RoxygenNote: 7.1.1

+RoxygenNote: 7.1.2

 BugReports: https://github.com/campbio/celda/issues

 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian

 NeedsCompilation: yes

@@ -507,8 +507,18 @@ setMethod(

       pseudocount = 1e-20

     )

-    # This part needs to be optimized

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

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

+    allCol <- paste0("col_", seq_len(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 and set names

+    estRmat <- estRmat[, allCol]

     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) {