normalized_counts: Return a size-factor normalized and (optionally)...

In ClusterGVis: One-Step to Cluster and Visualize Gene Expression Data

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

Description

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

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.

Value

Size-factor normalized, and optionally log-transformed, expression matrix.

Author(s)

https://github.com/cole-trapnell-lab/monocle3

matrix

ClusterGVis documentation built on April 4, 2025, 2:27 a.m.