Man pages for hredestig/pcaMethods
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... |
