mixOmics (version 5.0-4)

wrapper.rgcca: mixOmics wrapper for Regularised Generalised Canonical Correlation Analysis (rgcca)

Description

Wrapper function to perform Regularized Generalised Canonical Correlation Analysis (rGCCA), a generalised approach for the integration of multiple datasets. For more details, see the help(rgcca) from the RGCCA package.

Usage

wrapper.rgcca(data, 
design = 1 - diag(length(data)), 
tau = rep(1, length(data)),
  ncomp = rep(1, length(data)), 
  scheme = "centroid", 
  scale = TRUE, 
  init = "svd", 
  bias = TRUE, 
  tol = .Machine$double.eps, 
  verbose = FALSE)

Arguments

data

a list of data sets (called 'blocks') matching on the same samples. Data in the list should be arranged in samples x variables. NAs are not allowed.

design

numeric matrix of size (number of blocks) x (number of blocks) with only 0 or 1 values. A value of 1 (0) indicates a relationship (no relationship) between the blocks to be modelled using sGCCA.

tau

numeric vector of length the number of blocks in data. Each regularization parameter will be applied on each block and takes the value between 0 (no regularisation) and 1. If tau = "optimal" the shrinkage paramaters are estimated for each blo

ncomp

numeric vector of length the number of blocks in data. The number of components to include in the model for each block (does not necessarily takes the same value for each block).

scheme

Either "horst", "factorial" or "centroid" (Default: "centroid").

scale

If scale = TRUE, each block is standardized to zero means and unit variances (default: TRUE)

init

Mode of initialization use in the SGCCA algorithm, either by Singular Value Decompostion ("svd") or random ("random") (default : "svd").

bias

A logical value for biaised or unbiaised estimator of the var/cov (defaults to TRUE).

tol

Convergence stopping value.

verbose

if set to TRUE, reports progress on computing.

Value

• wrapper.rgcca returns an object of class "rgcca", a list that contains the following components:
• data
  the input data set (as a list).
• design
  the input design.
• variates
  the sgcca components.
• loadings
  the loadings for each block data set (outer wieght vector).
• loadings.star
  the laodings, standardised.
• tau
  the input tau parameter.
• scheme
  the input schme.
• ncomp
  the number of components on each block.
• crit
  the convergence criterion.
• AVE
  Indicators of model quality based on the Average Variance Explained (AVE): AVE(for one block), AVE(outer model), AVE(inner model)..
• names
  list containing the names to be used for individuals and variables.
• More details can be found in the references.

encoding

latin1

Details

This wrapper function performs rGCCA (see RGCCA) with $1, \ldots ,$ncomp components on each block data set. A supervised or unsupervised model can be run. For a supervised model, the unmap function should be used as an input data set. More details can be found on the package RGCCA.

References

Tenenhaus A. and Tenenhaus M., (2011), Regularized Generalized Canonical Correlation Analysis, Psychometrika, Vol. 76, Nr 2, pp 257-284. Schafer J. and Strimmer K., (2005), A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statist. Appl. Genet. Mol. Biol. 4:32.

See Also

rgcca, plotIndiv, plotVar, wrapper.sgcca. sgcca and http://www.mixOmics.org for more details.

Examples

data(nutrimouse)
# need to unmap the Y factor diet
Y = unmap(nutrimouse$diet)
data = list(nutrimouse$gene, nutrimouse$lipid,Y)
# with this design, gene expression and lipids are connected to the diet factor
# design = matrix(c(0,0,1,
#                   0,0,1,
#                   1,1,0), ncol = 3, nrow = 3, byrow = TRUE)

# with this design, gene expression and lipids are connected to the diet factor
# and gene expression and lipids are also connected
design = matrix(c(0,1,1,
                  1,0,1,
                  1,1,0), ncol = 3, nrow = 3, byrow = TRUE)
#note: the tau parameter is the regularization parameter
wrap.result.rgcca = wrapper.rgcca(data = data, design = design, tau = c(1, 1, 0), 
                                  ncomp = c(2, 2, 1),
                                  scheme = "centroid", verbose = FALSE)
#wrap.result.rgcca