monocle3 (version 1.0.0)

normalized_counts: Return a size-factor normalized and (optionally) log-transformed expression matrix

Description

Return a size-factor normalized and (optionally) log-transformed expression matrix

Usage

normalized_counts(
  cds,
  norm_method = c("log", "binary", "size_only"),
  pseudocount = 1
)

Arguments

cds

A CDS object to calculate normalized expression matrix from.

norm_method

String indicating the normalization method. Options are "log" (Default), "binary" and "size_only".

pseudocount

A pseudocount to add before log transformation. Ignored if norm_method is not "log". Default is 1.