A collection of PCA methods

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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