normalizeMethods {MsCoreUtils}R Documentation

Quantitative data normalisation

Description

Function to normalise a matrix of quantitative omics data. The nature of the normalisation is controlled by the method argument, described below.

Usage

normalizeMethods()

normalize_matrix(x, method, ...)

Arguments

x

A matrix to be normalised.

method

character(1) defining the normalisation method. See normalizeMethods() for available ones.

...

Additional parameters passed to the inner normalisation function.

Details

The method parameter can be one of "sum", "max", "center.mean", "center.median", "div.mean", "div.median", "diff.meda", "quantiles", "quantiles.robust" or "vsn". The normalizeMethods() function returns a vector of available normalisation methods.

Value

A normalised matrix of dimensions dim(x).

Author(s)

Laurent Gatto

See Also

The scale() function that centers (like center.mean above) and scales.

Examples

normalizeMethods()

## test data
set.seed(42)
m <- matrix(rlnorm(60), 10)

normalize_matrix(m, method = "sum")

normalize_matrix(m, method = "max")

normalize_matrix(m, method = "quantiles")

normalize_matrix(m, method = "center.mean")

[Package MsCoreUtils version 1.5.0 Index]