iSubGen (version 1.0.4)

calculate.scaling: Calculate scaling factors

Description

Calculate scaling factors

Usage

calculate.scaling(data.matrices);

Value

a list with two elements named: \"center\" and \"scale\", and each of these element is a named numerical vector or a list of named numerical vectors. If scaling.factors$center or scaling.factors$scale are a list then each element will correspond to a one of the data matrices. Finally, the named numerical vectors will match the row and rownames from the data matrices.

Arguments

data.matrices

list, where each element is a matrix. The list has one matrix for each data type to be scaled

Author

Natalie Fox

Details

The names for the data matrices and the center and scale lists all must match.

Examples

# Load molecular profiles for three data types from example files saved
# in the package as _profiles.txt
example.molecular.data.dir <- paste0(path.package('iSubGen'),'/exdata/');
molecular.data <- list();
for (i in c('cna','snv','methy')) {
  molecular.data[[i]] <- load.molecular.aberration.data(
    paste0(example.molecular.data.dir,i,'_profiles.txt'),
    patients = c(paste0('EP00',1:9), paste0('EP0',10:30))
    );
  }

# Example 1: Calculate scaling factors for all three data types
scaling.factors <- calculate.scaling(molecular.data);

# Example 2: Calculate scaling factors for only the methylation data
scaling.factors2 <- calculate.scaling(molecular.data[['methy']]);