Handling layer names

[wudustan]

I imported 11 separate bc_matrix objects from 10X and added them to a merged Seurat.

Layers(merge.seurat)
 [1] "counts.1"  "counts.2"  "counts.3"  "counts.4"  "counts.5"  "counts.6"  "counts.7"  "counts.8"  "counts.9"  "counts.10" "counts.11"

What is the correct way to assign a name to the counts so that they're identifiable rather than just having numbers?

> names(merge.seurat@assays$RNA)
NULL

> names(merge.seurat@assays$RNA@layers)
 [1] "counts.1"  "counts.2"  "counts.3"  "counts.4"  "counts.5"  "counts.6"  "counts.7"  "counts.8"  "counts.9"  "counts.10" "counts.11"

> Layers(merge.seurat) <- paste0("counts.", gsub("\\.NEW|\\.RNA", "", names(seurat.list)))
Error in Layers(merge.seurat) <- paste0("counts.", gsub("\\.NEW|\\.RNA",  : 
  could not find function "Layers<-"

names(merge.seurat@assays$RNA@layers) <- paste0("counts.", gsub("\\.NEW|\\.RNA", "", names(seurat.list)))

> merge.seurat <- NormalizeData(merge.seurat)
Normalizing layer: counts.SU.PSCG1
Error in match.arg(arg = i, choices = colnames(x = x)) : 
  'arg' should be one of "counts.1", "counts.2", "counts.3", "counts.4", "counts.5", "counts.6", "counts.7", "counts.8", "counts.9", 
"counts.10", "counts.11"