BPCA_dostep             Do BPCA estimation step
BPCA_initmodel          Initialize BPCA model
DModX,pcaRes-method     DModX
Q2                      Cross-validation for PCA
R2VX,pcaRes-method      R2 goodness of fit
R2cum,pcaRes-method     Cumulative R2 is the total ratio of variance
                        that is being explained by the model
RnipalsPca              NIPALS PCA implemented in R
asExprSet               Convert pcaRes object to an expression set
biplot-methods          Plot a overlaid scores and loadings plot
bpca                    Bayesian PCA missing value estimation
center,pcaRes-method    Get the centers of the original variables
centered,pcaRes-method
                        Check centering was part of the model
checkData               Do some basic checks on a given data matrix
completeObs,nniRes-method
                        Get the original data with missing values
                        replaced with predicted values.
cvseg                   Get CV segments
cvstat,pcaRes-method    Get cross-validation statistics (e.g. Q^2).
deletediagonals         Delete diagonals
derrorHierarchic        Later
dim.pcaRes              Dimensions of a PCA model
errorHierarchic         Later
fitted-methods          Extract fitted values from PCA.
forkNlpcaNet            Complete copy of nlpca net object
getHierarchicIdx        Index in hiearchy
helix                   A helix structured toy data set
kEstimate               Estimate best number of Components for missing
                        value estimation
kEstimateFast           Estimate best number of Components for missing
                        value estimation
leverage,pcaRes-method
                        Extract leverages of a PCA model
lineSearch              Line search for conjugate gradient
linr                    Linear kernel
listPcaMethods          List PCA methods
llsImpute               LLSimpute algorithm
loadings,ANY-method     Crude way to unmask the function with the same
                        name from 'stats'
loadings,pcaRes-method
                        Get loadings from a pcaRes object
loadings.pcaRes         Get loadings from a pcaRes object
metaboliteData          A incomplete metabolite data set from an
                        Arabidopsis coldstress experiment
metaboliteDataComplete
                        A complete metabolite data set from an
                        Arabidopsis coldstress experiment
method,pcaRes-method    Get the used PCA method
nObs,pcaRes-method      Get the number of observations used to build
                        the PCA model.
nP,pcaRes-method        Get number of PCs
nPcs,pcaRes-method      Get number of PCs.
nVar,pcaRes-method      Get the number of variables used to build the
                        PCA model.
nipalsPca               NIPALS PCA
nlpca                   Non-linear PCA
nmissing,pcaRes-method
                        Missing values
nni                     Nearest neighbour imputation
nniRes                  Class for representing a nearest neighbour
                        imputation result
optiAlgCgd              Conjugate gradient optimization
orth                    Calculate an orthonormal basis
pca                     Perform principal component analysis
pcaMethods              pcaMethods
pcaMethods-deprecated   Deprecated methods for pcaMethods
pcaNet                  Class representation of the NLPCA neural net
pcaRes                  Class for representing a PCA result
plot.pcaRes             Plot diagnostics (screeplot)
plotPcs                 Plot many side by side scores XOR loadings
                        plots
ppca                    Probabilistic PCA
predict-methods         Predict values from PCA.
prep                    Pre-process a matrix for PCA
rediduals-methods       Residuals values from a PCA model.
repmat                  Replicate and tile an array.
robustPca               PCA implementation based on robustSvd
robustSvd               Alternating L1 Singular Value Decomposition
sDev,pcaRes-method      Get the standard deviations of the scores
                        (indicates their relevance)
scaled,pcaRes-method    Check if scaling was part of the PCA model
scl,pcaRes-method       Get the scales (e.g. standard deviations) of
                        the original variables
scores,pcaRes-method    Get scores from a pcaRes object
scores.pcaRes           Get scores from a pcaRes object
show-methods            Print/Show for pcaRes
showNniRes              Print a nniRes model
simpleEllipse           Hotelling's T^2 Ellipse
slplot,pcaRes-method    Side by side scores and loadings plot
sortFeatures            Sort the features of NLPCA object
summary                 Summary of PCA model
svdImpute               SVDimpute algorithm
svdPca                  Perform principal component analysis using
                        singular value decomposition
tempFixNas              Temporary fix for missing values
vector2matrices,matrix-method
                        Tranform the vectors of weights to matrix
                        structure
vector2matrices,nlpcaNet-method
                        Tranform the vectors of weights to matrix
                        structure
wasna,pcaRes-method     Get a matrix with indicating the elements that
                        were missing in the input data. Convenient for
                        estimating imputation performance.
weightsAccount          Create an object that holds the weights for
                        nlpcaNet. Holds and sets weights in using an
                        environment object.
