Normalize data in a Seurat object — sn_normalize_data • Shennong

This function provides a unified normalization entry point for Seurat-style log-normalization, scran normalization, and SCTransform.

Usage

sn_normalize_data(
  object,
  method = c("seurat", "scran", "sctransform", "sct"),
  clusters = NULL,
  assay = "RNA",
  layer = "counts",
  ...
)

Arguments

object: A Seurat object.
method: One of "seurat", "scran", or "sctransform" (alias "sct").
clusters: Optional cluster assignments for scran::quickCluster.
assay: Assay used for normalization. Defaults to "RNA".
layer: Layer used as the input count matrix. Defaults to "counts".
...: Additional method-specific arguments passed to Seurat::NormalizeData(), scran::computeSumFactors(), or Seurat::SCTransform().

Value

A Seurat object with normalized data stored according to the chosen method.

Examples

if (FALSE) { # \dontrun{
seurat_obj <- sn_normalize_data(seurat_obj, method = "scran")
} # }