centre.scale.dataset {SIMMS}

Centre and scale a data matrix

Description

Centre and scale a data matrix. Scaling is done on each column separately

Usage

centre.scale.dataset(x = NULL, centre.data = "median")

Arguments

x

A sample by feature data matrix

centre.data

A character string specifying the centre value to be used for scaling data. Valid values are: 'median', 'mean', or a user defined numeric threshold e.g. '0.3' when modelling methylation beta values. This value is used for both scaling as well as for dichotomising data for estimating univariate betas from Cox model. Defaults to 'median'

Value

A centred and scaled data matrix

Author(s)

Syed Haider

Examples

tmp <- matrix(data = rnorm(100, 10, 2), nrow = 20);
tmp.scaled.median <- centre.scale.dataset(x = tmp);
tmp.scaled.mean <- centre.scale.dataset(x = tmp, centre.data = "mean");
tmp.scaled.custom <- centre.scale.dataset(x = tmp, centre.data = 0.3);