Centered Log-Ratio Normalization

This function performs Centered Log-Ratio (CLR) transformation on compositional data. CLR transforms each component by taking the logarithm of the ratio of the component to the geometric mean of all components. This is useful for analyzing compositional data where the relative proportions are of interest rather than absolute values.

Usage

normalize_clr(x)

# S3 method for class 'glyexp_experiment'
normalize_clr(x)

# S3 method for class 'matrix'
normalize_clr(x)

# Default S3 method
normalize_clr(x)

Arguments

x

Either a glyexp_experiment object or a matrix. If a matrix, rows should be variables and columns should be samples.

Value

Returns the same type as the input. If x is a glyexp_experiment, returns a glyexp_experiment with CLR-transformed expression matrix. If x is a matrix, returns a CLR-transformed matrix. Note that the resulting values are on the log scale and can be negative.

Details

The formula is: clr(x)_i = log(x_i / g(x)) where g(x) is the geometric mean of all components in the sample.

This function requires all values to be strictly positive (no zeros or NA values). Users must handle zeros and missing values before calling this function.

This function is a wrapper around compositions::clr().