Add back ribo filter

r.scripts/sc-TissueMapper_RAW.R

@@ -50,24 +50,24 @@ counts.cell.filtered.2mito <- results[[4]]
 counts.gene.filtered.2mito <- results[[5]]
 rm(results)
 
-#results <- scQC(sc10x,sp=opt$s,feature="percent.ribo")
-#sc10x <- results[[1]]
-#counts.cell.filtered.3ribo <- results[[4]]
-#counts.gene.filtered.3ribo <- results[[5]]
-#rm(results)
+results <- scQC(sc10x,sp=opt$s,feature="percent.ribo")
+sc10x <- results[[1]]
+counts.cell.filtered.3ribo <- results[[4]]
+counts.gene.filtered.3ribo <- results[[5]]
+rm(results)
 
 results <- scQC(sc10x,sp=opt$s,feature="nCount_RNA")
 sc10x <- results[[1]]
-counts.cell.filtered.3gene <- results[[4]]
-counts.gene.filtered.3gene <- results[[5]]
+counts.cell.filtered.4gene <- results[[4]]
+counts.gene.filtered.4gene <- results[[5]]
 rm(results)
 
 #sc10x <- lapply(sc10x,function(x) subset(x,subset= nCount_RNA>2500))
 #counts.cell.filtered.3gene <- lapply(sc10x,ncol)
 #counts.gene.filtered.3gene <- lapply(sc10x,nrow)
 
-counts.cell.filtered <- counts.cell.filtered.3gene
-counts.gene.filtered <- counts.gene.filtered.3gene
+counts.cell.filtered <- counts.cell.filtered.4gene
+counts.gene.filtered <- counts.gene.filtered.4gene
 
 save.image(file="./analysis/sc10x.raw_filtered.RData")