Closed zgb963 closed 7 months ago
Hi @zgb963,
You should use the SeuratObject::GetAssayData()
function.
filtered_combined_rhemac10_count_matrix <- SeuratObject::GetAssayData(object = seurat.obj_combined_filtered,
assay = "RNA",
layer = "counts")
Hope this helps!
Best, Leon
Hi @zgb963,
You should use the
SeuratObject::GetAssayData()
function.filtered_combined_rhemac10_count_matrix <- SeuratObject::GetAssayData(object = seurat.obj_combined_filtered, assay = "RNA", layer = "counts")
Hope this helps!
Best, Leon
Hi @leonfodoulian it worked, thank you!
Hi @zgb963,
Yes, as @leonfodoulian states GetAssayData
will work. However, for future GetAssayData
has been superseded by LayerData
which will do the same thing.
Best, Sam
Hi Seurat team,
How can I extract the full counts matrix from a seurat object (with rows as features/genes and columns as cell barcodes). My seurat object is below.
I basically just want to extract the sparse count matrix from this object so I can use it to run another software. I tried doing this below but it doesn't pull the genes names (rows) and the cell barcodes (columns)