mixOmics (version 6.2.0)

wrapper.sgcca: mixOmics wrapper for Sparse Generalised Canonical Correlation Analysis (sgcca)

Description

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

Usage

wrapper.sgcca(X,
design = 1 - diag(length(X)),
penalty = NULL,
ncomp = 1,
keepX.constraint,
keepX,
scheme = "horst",
mode="canonical",
scale = TRUE,
bias = TRUE,
init = "svd.single",
tol = .Machine$double.eps,
verbose = FALSE,
max.iter=1000,
near.zero.var = FALSE)

Arguments

X

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.

penalty

numeric vector of length the number of blocks in X. Each penalty parameter will be applied on each block and takes the value between 0 (no variable selected) and 1 (all variables included).

ncomp

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

keepX.constraint

A list of same length as X. Each entry keepX.constraint[[i]] is a list containing which variables of X[[i]] are to be kept on each of the first PLS-components

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").

mode

character string. What type of algorithm to use, (partially) matching one of "regression", "canonical", "invariant" or "classic". See Details.

scale

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

bias

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

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.

verbose

if set to TRUE, reports progress on computing.

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

Value

wrapper.sgcca returns an object of class "sgcca", 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.

penalty

the input penalty 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 sGCCA (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.

Note that this function is the same as block.spls with different default arguments.

More details about the PLS modes in ?pls.

References

Tenenhaus A. and Tenenhaus M., (2011), Regularized Generalized Canonical Correlation Analysis, Psychometrika, Vol. 76, Nr 2, pp 257-284.

Tenenhaus A., Phillipe C., Guillemot, V., Le Cao K-A., Grill J., Frouin, V. Variable Selection For Generalized Canonical Correlation Analysis. 2013. (in revision)

See Also

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

Examples

# NOT RUN {
data(nutrimouse)
# need to unmap the Y factor diet if you pretend this is not a classification pb.
# see also the function block.splsda for discriminant analysis  where you dont
# need to unmap Y.
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 penalty parameters will need to be tuned
wrap.result.sgcca = wrapper.sgcca(X = data, design = design, penalty = c(.3,.5, 1),
                                  ncomp = 2,
                                  scheme = "centroid", verbose = FALSE)
wrap.result.sgcca
#did the algo converge?
wrap.result.sgcca$crit  # yes
# }