Seurat (version 5.0.3)

LogNormalize: Normalize Raw Data

Description

Normalize Raw Data

Usage

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

Value

A matrix with the normalized and log-transformed data

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

Examples

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