mint.block.plsda: NP-integration with Discriminant Analysis

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

View source: R/mint.block.plsda.R

Description

Function to integrate data sets measured on the same samples (N-integration) and to combine multiple independent studies measured on the same variables or predictors (P-integration) using variants of multi-group and generalised PLS-DA for supervised classification.

Usage

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mint.block.plsda(
  X,
  Y,
  indY,
  study,
  ncomp = 2,
  design,
  scheme,
  scale = TRUE,
  init,
  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 samples x variables, with samples order matching in all data sets.

Y

A factor or a class vector indicating the discrete outcome of each sample.

indY

To be supplied if Y is missing, indicates the position of the matrix / vector response in the list X

study

Factor, indicating the membership of each sample to each of the studies being combined

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

The function fits multi-group generalised PLS models with a specified number of ncomp components. 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 more details in ?pls).

Value

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

X

the centered and standardized original predictor matrix.

Y

the centered and standardized original response vector or matrix.

ncomp

the number of components included in the model for each block.

mode

the algorithm used to fit the model.

mat.c

matrix of coefficients from the regression of X / residual matrices X on the X-variates, to be used internally by predict.

variates

list containing the X and Y variates.

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.

tol

the tolerance used in the iterative algorithm, used for subsequent S3 methods

max.iter

the maximum number of iterations, used for subsequent S3 methods

iter

Number of iterations of the algorthm for each component

Author(s)

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

References

On multi-group PLS:

Rohart F, Eslami A, Matigian, N, Bougeard S, Lê Cao K-A (2017). MINT: A multivariate integrative approach to identify a reproducible biomarker signature across multiple experiments and platforms. BMC Bioinformatics 18:128.

Eslami, A., Qannari, E. M., Kohler, A., and Bougeard, S. (2014). Algorithms for multi-group PLS. J. Chemometrics, 28(3), 192-201.

On multiple integration with PLSDA:

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

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.

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

spls, summary, plotIndiv, plotVar, predict, perf, mint.block.spls, mint.block.plsda, mint.block.splsda and http://www.mixOmics.org/mixMINT for more details.

Examples

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data(breast.TCGA)

# for the purpose of this example, we consider the training set as study1 and
# the test set as another independent study2.
study = c(rep("study1",150), rep("study2",70))

mrna = rbind(breast.TCGA$data.train$mrna, breast.TCGA$data.test$mrna)
mirna = rbind(breast.TCGA$data.train$mirna, breast.TCGA$data.test$mirna)
data = list(mrna = mrna, mirna = mirna)

Y = c(breast.TCGA$data.train$subtype, breast.TCGA$data.test$subtype)

res = mint.block.plsda(data,Y,study=study, ncomp=2)

res

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