normalize: Quantitative data normalisation

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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

Usage

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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

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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")

MsCoreUtils documentation built on Nov. 8, 2020, 10:59 p.m.