BPCA_dostep             Do BPCA estimation step
BPCA_initmodel          Initialize BPCA model
DModX                   DModX
Q2                      Cross-validation for PCA
R2cum                   Cumulative R2 is the total ratio of variance
                        that is being...
RnipalsPca              NIPALS PCA implemented in R
asExprSet               Convert pcaRes object to an expression set
biplot,pcaRes-method    Biplot for pcaRes method.
biplot.pcaRes           Plot a overlaid scores and loadings plot
bpca                    Bayesian PCA Missing Value Estimator
center                  Get the centers of the original variables...
centered                Check centering was part of the model...
checkData               Do some basic checks on a given data matrix
completeObs             Get the original data with missing values
                        replaced with predicted...
cvstat                  Get cross-validation statistics (e...
deletediagonals         Delete diagonals
derrorHierarchic        Later...
dim.pcaRes              Dimensions of a PCA model...
errorHierarchic         Later...
fitted,pcaRes-method    Fitted PCA data.
fitted.pcaRes           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                Extract leverages of a PCA model
lineSearch              Line search for conjugate gradient...
linr                    Linear kernel...
listPcaMethods          List PCA methods
llsImpute               LLSimpute algorithm
loadings.pcaRes         Get the loadings from a PCA model...
metaboliteData          A incomplete metabolite data set from an
                        Arabidopsis coldstress
metaboliteDataComplete
                        A complete metabolite data set from an
                        Arabidopsis coldstress
method                  Get the used PCA method...
nObs                    Get the number of observations used to build
                        the PCA model.
nP                      Get number of PCs...
nPcs                    Get number of PCs.
nVar                    Get the number of variables used to build the
                        PCA model.
nipalsPca               NIPALS PCA
nlpca                   Non-linear PCA
nlpcaNet                Class representation of the NLPCA neural net
nmissing                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
pcaRes                  Class for representing a PCA result
plot.pcaRes             Plot diagnostics (screeplot)
plotPcs                 Plot many side by side scores XOR loadings
                        plots
plotR2                  R2 plot (screeplot) for PCA
ppca                    Probabilistic PCA
predict,pcaRes-method   Predict PCA data.
predict.pcaRes          Predict values from PCA.
prep                    Pre-process a matrix for PCA
print,pcaRes-method     Print basic info...
repmat                  Replicate and tile an array.
resid,pcaRes-method     Residuals of PCA data.
residuals,pcaRes-method
                        Residuals of PCA data.
residuals.pcaRes        Residuals values from a PCA model.
robustPca               PCA implementation based on robustSvd
robustSvd               Alternating L1 Singular Value Decomposition
sDev                    Get the standard deviations of the scores
                        (indicates their...
scaled                  Check if scaling was part of the PCA model...
scl                     Get the scales (e...
scores.pcaRes           Get the scores from a PCA model...
show,pcaRes-method      Show pcaRes / nniRes objects.
showNniRes              Print a nniRes model
showPcaRes              Print/Show for pcaRes
simpleEllipse           Hotelling's T^2 Ellipse
slplot                  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...
wasna                   Get a matrix with indicating the elements that
                        were missing in the...
weightsAccount          Create an object that holds the weights for
                        nlpcaNet.
