Normalize Expression Data in SCE/SPE Objects

Adds a normalized assay (cpm, logcpm, or logpf) to a SingleCellExperiment or SpatialExperiment. The original assay is left unchanged. cpm computes counts per million, logcpm is log(cpm + 1), and logpf is log((counts + 1) / (gene_mean + 1)) with gene-wise means computed from counts + 1.

Usage

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

Arguments

object

A SingleCellExperiment or SpatialExperiment with raw counts.

method

Normalization method: "cpm", "logcpm", or "logpf".

assay

Assay to normalize (default: "counts").