@@ -246,6 +246,8 @@ setMethod("decontX", "ANY", function(x,

     # Remove cells with the same ID between x and the background matrix

     background <- .checkBackground(x = x, background = background,

                                    logfile = logfile, verbose = verbose)

+

+    countsBackground <- background

   }

   .decontX(

@@ -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) {