block.spls: N-integration and feature selection with sparse Projection to...
In mixOmicsTeam/mixOmics: Omics Data Integration Project

block.spls

R Documentation

N-integration and feature selection with sparse Projection to Latent Structures models (sPLS)

Description

Integration of multiple data sets measured on the same samples or observations, with variable selection in each data set, ie. N-integration. The method is partly based on Generalised Canonical Correlation Analysis.

Usage

block.spls(
  X,
  Y,
  indY,
  ncomp = 2,
  keepX,
  keepY,
  design,
  mode,
  scale = TRUE,
  tol = 1e-06,
  max.iter = 100,
  near.zero.var = FALSE,
  all.outputs = TRUE,
  verbose.call = FALSE
)

Arguments

`X`	A named list of data sets (called 'blocks') measured on the same samples. Data in the list should be arranged in matrices, samples x variables, with samples order matching in all data sets.
`Y`	Matrix response for a multivariate regression framework. Data should be continuous variables (see `?block.splsda` for supervised classification and factor response).
`indY`	To supply if `Y` is missing, indicates the position of the matrix response in the list `X`.
`ncomp`	the number of components to include in the model. Default to 2. Applies to all blocks.
`keepX`	A named list of same length as X. Each entry is the number of variables to select in each of the blocks of X for each component. By default all variables are kept in the model.
`keepY`	Only if Y is provided (and not `indY`). Each entry is the number of variables to select in each of the blocks of Y for each component.
`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; a value of 0 indicates no relationship, 1 is the maximum value. Alternatively, one of c('null', 'full') indicating a disconnected or fully connected design, respecively, or a numeric between 0 and 1 which will designate all off-diagonal elements of a fully connected design (see examples in `block.splsda`). If `Y` is provided instead of `indY`, the `design` matrix is changed to include relationships to `Y`.
`mode`	Character string indicating the type of PLS algorithm to use. One of `"regression"`, `"canonical"`, `"invariant"` or `"classic"`. See Details.
`scale`	Logical. If scale = TRUE, each block is standardized to zero means and unit variances (default: TRUE)
`tol`	Positive numeric used as convergence criteria/tolerance during the iterative process. Default to `1e-06`.
`max.iter`	Integer, the maximum number of iterations. Default to 100.
`near.zero.var`	Logical, 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`	Logical. Computation can be faster when some specific (and non-essential) outputs are not calculated. Default = `TRUE`.
`verbose.call`	Logical (Default=FALSE), if set to TRUE then the `$call` component of the returned object will contain the variable values for all parameters. Note that this may cause large memory usage.

Details

block.spls function fits a horizontal sPLS model with a specified number of components per block). An outcome needs to be provided, either by Y or by its position indY in the list of blocks X. Multi (continuous)response are supported. X and Y can contain missing values. Missing values are handled by being disregarded during the cross product computations in the algorithm block.pls without having to delete rows with missing data. Alternatively, missing data can be imputed prior using the nipals function.

The type of algorithm to use is specified with the mode argument. Four PLS algorithms are available: PLS regression ("regression"), PLS canonical analysis ("canonical"), redundancy analysis ("invariant") and the classical PLS algorithm ("classic") (see References and ?pls for more details).

Note that our method is partly based on sparse Generalised Canonical Correlation Analysis and differs from the MB-PLS approaches proposed by Kowalski et al., 1989, J Chemom 3(1), Westerhuis et al., 1998, J Chemom, 12(5) and sparse variants Li et al., 2012, Bioinformatics 28(19); Karaman et al (2014), Metabolomics, 11(2); Kawaguchi et al., 2017, Biostatistics.

Variable selection is performed on each component for each block of X, and for Y if specified, via input parameter keepX and keepY.

Note that if Y is missing and indY is provided, then variable selection on Y is performed by specifying the input parameter directly in keepX (no keepY is needed).

Value

block.spls returns an object of class "block.spls", a list that contains the following components:

`X`	the centered and standardized original predictor matrix.
`indY`	the position of the outcome Y in the output list X.
`ncomp`	the number of components included in the model for each block.
`mode`	the algorithm used to fit the model.
`keepX`	Number of variables used to build each component of each block
`keepY`	Number of variables used to build each component of Y
`variates`	list containing the variates of each block of X.
`loadings`	list containing the estimated loadings for the variates.
`names`	list containing the names to be used for individuals and variables.
`nzv`	list containing the zero- or near-zero predictors information.
`iter`	Number of iterations of the algorithm for each component
`prop_expl_var`	Percentage of explained variance for each component and each block after setting possible missing values in the centered data to zero
`call`	if `verbose.call = FALSE`, then just the function call is returned. If `verbose.call = TRUE` then all the inputted values are accessable via this component

Note that the argument 'scheme' has now been hardcoded to 'horst' and 'init' to 'svd.single'.

Author(s)

Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao, Al J Abadi

References

Tenenhaus, M. (1998). La regression PLS: theorie et pratique. Paris: Editions Technic.

Wold H. (1966). Estimation of principal components and related models by iterative least squares. In: Krishnaiah, P. R. (editors), Multivariate Analysis. Academic Press, N.Y., 391-420.

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

Tenenhaus A., Philippe C., Guillemot V, Lê Cao K.A., Grill J, Frouin V. Variable selection for generalized canonical correlation analysis. Biostatistics. kxu001

Examples

# Example with multi omics TCGA study
# -----------------------------
data("breast.TCGA")
# this is the X data as a list of mRNA and miRNA; the Y data set is a single data set of proteins
data = list(mrna = breast.TCGA$data.train$mrna, mirna = breast.TCGA$data.train$mirna)
# set up a full design where every block is connected
design = matrix(1, ncol = length(data), nrow = length(data),
dimnames = list(names(data), names(data)))
diag(design) =  0
design
# set number of component per data set
ncomp = c(2)
# set number of variables to select, per component and per data set (this is set arbitrarily)
list.keepX = list(mrna = rep(10, 2), mirna = rep(10,2))
list.keepY = c(rep(10, 2))

TCGA.block.spls = block.spls(X = data, Y = breast.TCGA$data.train$protein,
ncomp = ncomp, keepX = list.keepX, keepY = list.keepY, design = design)
TCGA.block.spls
# in plotindiv we color the samples per breast subtype group but the method is unsupervised!
plotIndiv(TCGA.block.spls, group =  breast.TCGA$data.train$subtype, ind.names = FALSE, legend=TRUE)
# illustrates coefficient weights in each block
plotLoadings(TCGA.block.spls, ncomp = 1)
plotVar(TCGA.block.spls, style = 'graphics', legend = TRUE)

## plot markers (selected markers) for mrna and mirna
group <- breast.TCGA$data.train$subtype
# mrna: show each selected feature separately and group by subtype
plotMarkers(object = TCGA.block.spls, comp = 1, block = 'mrna', group = group)
# mrna: aggregate all selected features, separate by loadings signs and group by subtype
plotMarkers(object = TCGA.block.spls, comp = 1, block = 'mrna', group = group, global = TRUE)
# proteins
plotMarkers(object = TCGA.block.spls, comp = 1, block = 'Y', group = group)
## only show boxplots
plotMarkers(object = TCGA.block.spls, comp = 1, block = 'Y', group = group, violin = FALSE)

## Not run: 
network(TCGA.block.spls)

## End(Not run)

mixOmicsTeam/mixOmics documentation built on Nov. 19, 2024, 11:53 a.m.