Normalize Gene Expression Data in SingleCellExperiment or SpatialExperiment Objects

This function applies normalization to the gene expression data stored within a SingleCellExperiment or SpatialExperiment object. It supports both counts per million (CPM) and log-transformed counts per million (logCPM) normalization methods.

Usage

normalize(object, method = "cpm", assay = "counts")

Arguments

object

A SingleCellExperiment or SpatialExperiment object containing raw gene expression data.

method

The normalization method to apply: "cpm" for counts per million, "logcpm" for log-transformed counts per million, or "logpf" for log-proportional factor.

assay

The name of the assay to normalize, default "counts".