LogNormalize {Seurat}

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