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(X,
    design = 1 - diag(length(X)),
    tau = rep(1, length(X)),
    ncomp = 1,
    keepX,
    scheme = "horst",
    scale = TRUE,
    init = "svd.single",
    tol = .Machine$double.eps,
    max.iter=1000,
    near.zero.var = FALSE,
    all.outputs = TRUE)

Arguments

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 in X) x (number of blocks in X) with values between 0 and 1. Each value indicates the strenght of the relationship to be modelled between two blocks using sGCCA; a value of 0 indicates no relationship, 1 is the maximum value. If Y is provided instead of indY, the design matrix is changed to include relationships to Y.

tau

numeric vector of length the number of blocks in X. 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 block and each dimension using the Schafer and Strimmer (2005) analytical formula.

ncomp

the number of components to include in the model. Default to 1.

keepX

A vector of same length as X. Each entry keepX[i] is the number of X[[i]]-variables kept in the model on the last components (once all keepX.constraint[[i]] are used).

scheme

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

scale

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

init

Mode of initialization use in the algorithm, either by Singular Value Decompostion of the product of each block of X with Y ("svd") or each block independently ("svd.single") . Default to "svd.single".

tol

Convergence stopping value.

max.iter

integer, the maximum number of iterations.

near.zero.var

boolean, see the internal nearZeroVar function (should be set to TRUE in particular for data with many zero values). Setting this argument to FALSE (when appropriate) will speed up the computations. Default value is FALSE

all.outputs

boolean. Computation can be faster when some specific (and non-essential) outputs are not calculated. Default = TRUE.

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 included in the model for 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.

Details

This wrapper function performs rGCCA (see RGCCA) with $1, \dots,$ 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.

Examples

Run this code

# NOT RUN {
data(nutrimouse)
# need to unmap the Y factor diet
Y = unmap(nutrimouse$diet)
data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid, Y = 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(X = data, design = design, tau = c(1, 1, 0),
                                  ncomp = 2,
                                  scheme = "centroid")
#wrap.result.rgcca
# }

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