@@ -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

@@ -495,22 +495,21 @@ setMethod(

       z = as.integer(res$z),

       pseudocount = 1e-20

     )

-    

+

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

-    

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

+    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

     estRmat <- estRmat[, allCol]

-    

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

+

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

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

     resBatch[[bat]] <- list(