block.plsda: N-integration with Projection to Latent Structures models...

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/block.plsda.R

Description

Integration of multiple data sets measured on the same samples or observations to classify a discrete outcome, ie. N-integration with Discriminant Analysis. The method is partly based on Generalised Canonical Correlation Analysis.

Usage

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block.plsda(
  X,
  Y,
  indY,
  ncomp = 2,
  design,
  scheme,
  scale = TRUE,
  init = "svd",
  tol = 1e-06,
  max.iter = 100,
  near.zero.var = FALSE,
  all.outputs = TRUE
)

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

a factor or a class vector for the discrete outcome.

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.

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. If Y is provided instead of indY, the design matrix is changed to include relationships to Y.

scheme

Character, one of 'horst', 'factorial' or 'centroid'. Default = 'horst', see reference.

scale

Logical. 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 Decomposition of the product of each block of X with Y ('svd') or each block independently ('svd.single'). Default = svd.single.

tol

Numeric, convergence stopping value.

max.iter

Integer, the maximum number of iterations.

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.

Details

block.plsda function fits a horizontal integration PLS-DA model with a specified number of components per block). A factor indicating the discrete outcome needs to be provided, either by Y or by its position indY in the list of blocks X.

X 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 Generalised Canonical Correlation Analysis and differs from the MB-PLS approaches proposed by Kowalski et al., 1989, J Chemom 3(1) and Westerhuis et al., 1998, J Chemom, 12(5).

Value

block.plsda returns an object of class "block.plsda","block.pls", 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.

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 algorthm for each component

explained_variance

Percentage of explained variance for each component and each block

Author(s)

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

References

On PLSDA:

Barker M and Rayens W (2003). Partial least squares for discrimination. Journal of Chemometrics 17(3), 166-173. Perez-Enciso, M. and Tenenhaus, M. (2003). Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach. Human Genetics 112, 581-592. Nguyen, D. V. and Rocke, D. M. (2002). Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 18, 39-50.

On multiple integration with PLS-DA: Gunther O., Shin H., Ng R. T. , McMaster W. R., McManus B. M. , Keown P. A. , Tebbutt S.J. , Lê Cao K-A. , (2014) Novel multivariate methods for integration of genomics and proteomics data: Applications in a kidney transplant rejection study, OMICS: A journal of integrative biology, 18(11), 682-95.

On multiple integration with sPLS-DA and 4 data blocks:

Singh A., Gautier B., Shannon C., Vacher M., Rohart F., Tebbutt S. and Lê Cao K.A. (2016). DIABLO: multi omics integration for biomarker discovery. BioRxiv available here: http://biorxiv.org/content/early/2016/08/03/067611

mixOmics article:

Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for 'omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752

See Also

plotIndiv, plotArrow, plotLoadings, plotVar, predict, perf, selectVar, block.pls, block.splsda and http://www.mixOmics.org for more details.

Examples

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data(nutrimouse)
data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid, Y = nutrimouse$diet)
# with this design, all blocks are connected
design = matrix(c(0,1,1,1,0,1,1,1,0), ncol = 3, nrow = 3,
byrow = TRUE, dimnames = list(names(data), names(data)))

res = block.plsda(X = data, indY = 3) # indY indicates where the outcome Y is in the list X
plotIndiv(res, ind.names = FALSE, legend = TRUE)
plotVar(res)

## Not run: 
# when Y is provided
res2 = block.plsda(list(gene = nutrimouse$gene, lipid = nutrimouse$lipid),
Y = nutrimouse$diet, ncomp = 2)
plotIndiv(res2)
plotVar(res2)

## End(Not run)

mixOmics documentation built on Nov. 8, 2020, 11:12 p.m.