asExprSet | Convert pcaRes object to an expression set |
biplot-methods | Plot a overlaid scores and loadings plot |
bpca | Bayesian PCA missing value estimation |
BPCA_dostep | Do BPCA estimation step |
BPCA_initmodel | Initialize BPCA model |
centered-pcaRes-method | Check centering was part of the model |
center-pcaRes-method | Get the centers of the original variables |
checkData | Do some basic checks on a given data matrix |
completeObs-nniRes-method | Get the original data with missing values replaced with... |
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 |
DModX-pcaRes-method | DModX |
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... |
kEstimateFast | Estimate best number of Components for missing value... |
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... |
loadings.pcaRes | Get loadings from a pcaRes object |
loadings-pcaRes-method | Get loadings from a pcaRes object |
metaboliteData | A incomplete metabolite data set from an Arabidopsis... |
metaboliteDataComplete | A complete metabolite data set from an Arabidopsis coldstress... |
method-pcaRes-method | Get the used PCA method |
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 |
nObs-pcaRes-method | Get the number of observations used to build the PCA model. |
nPcs-pcaRes-method | Get number of PCs. |
nP-pcaRes-method | Get number of PCs |
nVar-pcaRes-method | Get the number of variables used to build the PCA model. |
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 |
Q2 | Cross-validation for PCA |
R2cum-pcaRes-method | Cumulative R2 is the total ratio of variance that is being... |
R2VX-pcaRes-method | R2 goodness of fit |
rediduals-methods | Residuals values from a PCA model. |
repmat | Replicate and tile an array. |
RnipalsPca | NIPALS PCA implemented in R |
robustPca | PCA implementation based on robustSvd |
robustSvd | Alternating L1 Singular Value Decomposition |
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... |
scores.pcaRes | Get scores from a pcaRes object |
scores-pcaRes-method | Get scores from a pcaRes object |
sDev-pcaRes-method | Get the standard deviations of the scores (indicates their... |
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... |
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... |
weightsAccount | Create an object that holds the weights for nlpcaNet. Holds... |
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