mint.block.splsda: NP-integration with Discriminant Analysis and variable...
In ajabadi/mixOmics2: Omics Data Integration Project

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

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 sparse multi-group and generalised PLS-DA for supervised classification and variable selection.

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mint.block.splsda(X, Y, indY, study, ncomp = 2, keepX, design, scheme,
  mode, scale = TRUE, init, tol = 1e-06, max.iter = 100,
  near.zero.var = FALSE, all.outputs = TRUE)

`X`	A 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`	Number of components to include in the model (see Details). Default to 2.
`keepX`	A 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.
`design`	numeric matrix of size (number of blocks in X) x (number of blocks in X) with 0 or 1 values. A value of 1 (0) indicates a relationship (no relationship) between the blocks to be modelled. If `Y` is provided instead of `indY`, the `design` matrix is changed to include relationships to `Y`.
`scheme`	Either "horst", "factorial" or "centroid". Default = `horst`, see reference.
`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)
`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 = `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`.

The function fits sparse multi-group generalised PLS Discriminant Analysis 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).

mint.block.splsda returns an object of class "mint.splsda", "block.splsda", 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

Florian Rohart, Benoit Gautier, Kim-Anh Lê Cao

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 sparse 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

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

## Not run: 

# 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.splsda(data,Y,study=study,
keepX = list(mrna=c(10,10), mirna=c(20,20)),ncomp=2)

res


## End(Not run)