debug when there is no NonUniqueCounts

Author: SuiYue-2308

R/bambu-assignDist.R

@@ -89,16 +89,22 @@ generateNonUniqueCounts <- function(readClassDt, countMatrix, annotations){
     if(nrow(x)>1 & length(unique(x$gene_sid))>1){
         nonuniqueCounts.gene <- sparse.model.matrix(~ factor(x$gene_sid) - 1)
         nonuniqueCounts <- t(nonuniqueCounts.gene) %*% nonuniqueCounts
+        #covert ids into gene ids
+        geneids <- as.numeric(levels(factor(x$gene_sid)))
+        geneids <- x$txid[match(geneids, x$gene_sid)]
+        geneids <- mcols(annotations)$GENEID[as.numeric(geneids)]
+        rownames(nonuniqueCounts) <- geneids
     } else{
         warning("The factor variable 'gene_sid' has only one level. Adjusting output.")
         nonuniqueCounts.gene <- Matrix(1, nrow = nrow(x), ncol = 1, sparse = TRUE)
         nonuniqueCounts <- t(nonuniqueCounts.gene) %*% nonuniqueCounts
+        #covert ids into gene ids
+        geneids <- as.numeric(levels(factor(x$gene_sid)))
+        geneids <- x$txid[match(geneids, x$gene_sid)]
+        geneids <- mcols(annotations)$GENEID[as.numeric(geneids)]
+        rownames(nonuniqueCounts) <- rownames(geneMat)[1:nrow(nonuniqueCounts)]
+
     }
-    #covert ids into gene ids
-    geneids <- as.numeric(levels(factor(x$gene_sid)))
-    geneids <- x$txid[match(geneids, x$gene_sid)]
-    geneids <- mcols(annotations)$GENEID[as.numeric(geneids)]
-    rownames(nonuniqueCounts) <- geneids
     #create matrix for all annotated genes
     genes <- levels(factor(unique(mcols(annotations)$GENEID)))
     geneMat <- sparseMatrix(length(genes), ncol(nonuniqueCounts), x = 0)