pls.lda.cv {plsgenomics} | R Documentation |
The function pls.lda.cv
determines the best number of latent components to be used for classification
with PLS dimension reduction and linear discriminant analysis as described in
Boulesteix (2004).
pls.lda.cv(Xtrain, Ytrain, ncomp, nruncv=20, alpha=2/3, priors=NULL)
Xtrain |
a (ntrain x p) data matrix containing the predictors for the training data set.
Xtrain may be a matrix or a data frame. Each row is an observation and each column is a
predictor variable. |
Ytrain |
a vector of length ntrain giving the classes of the ntrain observations. The classes must be coded as 1,...,K (K>=2). |
ncomp |
the vector of integers from which the best number of latent
components has to be chosen by cross-validation. If ncomp is of length
1, the best number of components is chosen from 1,...,ncomp . |
nruncv |
the number of cross-validation iterations to be performed for the choice of the number of latent components. |
alpha |
the proportion of observations to be included in the training set at each cross-validation iteration. |
priors |
The class priors to be used for linear discriminant analysis. If unspecified, the class proportions in the training set are used. |
The cross-validation procedure described in Boulesteix (2004) is used to
determine the best number of latent components to be used for classification.
At each cross-validation run, Xtrain
is split into a pseudo training
set and a pseudo test set and the classification error rate is determined for each
number of latent components. Finally, the function pls.lda.cv
returns
the number of latent components for which the mean classification rate over
the nrun
partitions is minimal.
The number of latent components to be used for classification.
Anne-Laure Boulesteix (http://www.slcmsr.net/boulesteix)
A. L. Boulesteix (2004). PLS dimension reduction for classification with microarray data, Statistical Applications in Genetics and Molecular Biology 3, Issue 1, Article 33.
A. L. Boulesteix, K. Strimmer (2007). Partial least squares: a versatile tool for the analysis of high-dimensional genomic data. Briefings in Bioinformatics 7:32-44.
S. de Jong (1993). SIMPLS: an alternative approach to partial least squares regression, Chemometrics Intell. Lab. Syst. 18, 251–263.
# load plsgenomics library library(plsgenomics) # load leukemia data data(leukemia) # Determine the best number of components to be used for classification using the cross-validation procedure # choose the best number from 2,3,4 pls.lda.cv(Xtrain=leukemia$X,Ytrain=leukemia$Y,ncomp=2:4,nruncv=20) # choose the best number from 1,2,3 pls.lda.cv(Xtrain=leukemia$X,Ytrain=leukemia$Y,ncomp=3,nruncv=20)