plsda: Partial Least Squares Discriminant Analysis (PLS-DA).

In mixOmics: Omics Data Integration Project

Description

Function to perform standard Partial Least Squares regression to classify samples.

Usage

plsda(X,
Y,
ncomp = 2,
scale = TRUE,
mode = c("regression", "canonical", "invariant", "classic"),
tol = 1e-06,
max.iter = 100,
near.zero.var = FALSE,
logratio="none",  # one of "none", "CLR"
multilevel=NULL,
all.outputs = TRUE)

Arguments

X	numeric matrix of predictors. NAs are allowed.
Y	a factor or a class vector for the discrete outcome.
ncomp	the number of components to include in the model. Default to 2.
scale	boleean. If scale = TRUE, each block is standardized to zero means and unit variances (default: TRUE)
mode	character string. What type of algorithm to use, (partially) matching one of "regression", "canonical", "invariant" or "classic". See Details.
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
logratio	one of ('none','CLR') specifies the log ratio transformation to deal with compositional values that may arise from specific normalisation in sequencing dadta. Default to 'none'
multilevel	sample information for multilevel decomposition for repeated measurements. A numeric matrix or data frame indicating the repeated measures on each individual, i.e. the individuals ID. See examples in ?splsda.
all.outputs	boolean. Computation can be faster when some specific (and non-essential) outputs are not calculated. Default = TRUE.

Details

plsda function fit PLS models with 1,...,ncomp components to the factor or class vector Y. The appropriate indicator matrix is created.

logratio transform and multilevel analysis are performed sequentially as internal pre-processing step, through logratio.transfo and withinVariation respectively.

Logratio can only be applied if the data do not contain any 0 value (for count data, we thus advise the normalise raw data with a 1 offset).

More details about the PLS modes in ?pls.

Value

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

X	the centered and standardized original predictor matrix.
Y	the centered and standardized indicator response vector or matrix.
ind.mat	the indicator matrix.
ncomp	the number of components included in the model.
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
explained_variance	amount of variance explained per component (note that contrary to PCA, this amount may not decrease as the aim of the method is not to maximise the variance, but the covariance between X and the dummy matrix Y).
mat.c	matrix of coefficients from the regression of X / residual matrices X on the X-variates, to be used internally by predict.
defl.matrix	residual matrices X for each dimension.

Author(s)

Ignacio González, Kim-Anh Lê Cao.

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 log ratio transformation:

Filzmoser, P., Hron, K., Reimann, C.: Principal component analysis for compositional data with outliers. Environmetrics 20(6), 621-632 (2009)

Lê Cao K.-A., Costello ME, Lakis VA, Bartolo, F,Chua XY, Brazeilles R, Rondeau P. MixMC: Multivariate insights into Microbial Communities. PLoS ONE, 11(8): e0160169 (2016).

On multilevel decomposition: Westerhuis, J.A., van Velzen, E.J., Hoefsloot, H.C., Smilde, A.K.: Multivariate paired data analysis: multilevel plsda versus oplsda. Metabolomics 6(1), 119-128 (2010)

Liquet, B., Lê Cao K.-A., Hocini, H., Thiebaut, R.: A novel approach for biomarker selection and the integration of repeated measures experiments from two assays. BMC bioinformatics 13(1), 325 (2012)

See Also

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

Examples

## First example
data(breast.tumors)
X <- breast.tumors$gene.exp
Y <- breast.tumors$sample$treatment

plsda.breast <- plsda(X, Y, ncomp = 2)
plotIndiv(plsda.breast, ind.names = TRUE, ellipse = TRUE, legend = TRUE)

## Not run: 
## Second example
data(liver.toxicity)
X <- liver.toxicity$gene
Y <- liver.toxicity$treatment[, 4]

plsda.liver <- plsda(X, Y, ncomp = 2)
plotIndiv(plsda.liver, ind.names = Y, ellipse = TRUE, legend =TRUE)


## End(Not run)

Example output

Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2

Loaded mixOmics 6.1.3

Visit http://www.mixOmics.org for more details about our methods.
Any bug reports or comments? Notify us at mixomics at math.univ-toulouse.fr or https://bitbucket.org/klecao/package-mixomics/issues

Thank you for using mixOmics!
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

mixOmics documentation built on June 1, 2018, 5:06 p.m.