LogNormalize: Normalize Raw Data

In Seurat: Tools for Single Cell Genomics

Normalize Raw Data

Description

Normalize Raw Data

Usage

LogNormalize(data, scale.factor = 10000, margin = 2L, verbose = TRUE, ...)

## S3 method for class 'data.frame'
LogNormalize(data, scale.factor = 10000, margin = 2L, verbose = TRUE, ...)

## S3 method for class 'V3Matrix'
LogNormalize(data, scale.factor = 10000, margin = 2L, verbose = TRUE, ...)

## Default S3 method:
LogNormalize(data, scale.factor = 10000, margin = 2L, verbose = TRUE, ...)

Arguments

data	Matrix with the raw count data
scale.factor	Scale the data; default is 1e4
margin	Margin to normalize over
verbose	Print progress
...	Arguments passed to other methods

Value

A matrix with the normalized and log-transformed data

Examples

mat <- matrix(data = rbinom(n = 25, size = 5, prob = 0.2), nrow = 5)
mat
mat_norm <- LogNormalize(data = mat)
mat_norm

Seurat documentation built on May 29, 2024, 4:20 a.m.