getCountMtxFromSeurat Extract count matrix from Seurat object (V4 and V5 compatible) — getCountMtxFromSeurat • SCEVAN

This function extracts the raw count matrix from a Seurat object, supporting both Seurat V4 and V5 data structures. It prioritizes V4 format.

Usage

getCountMtxFromSeurat(seurat_obj, assay = "RNA", layer = "counts")

Arguments

seurat_obj: A Seurat object
assay: Assay name to use (default "RNA")
layer: Layer name for Seurat V5 (default "counts")

Value

Raw count matrix with genes on rows and cells on columns

Examples

if (FALSE) { # \dontrun{
count_mtx <- getCountMtxFromSeurat(seurat_obj)
results <- pipelineCNA(count_mtx)
} # }