A collection of PCA methods.


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Documentation for package ‘pcaMethods’ version 1.24.0

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asExprSet Convert pcaRes object to an expression set
biplot,pcaRes-method Plot a overlaid scores and loadings plot
biplot.pcaRes Plot a overlaid scores and loadings plot
bpca Bayesian PCA Missing Value Estimator
centered Class for representing a PCA result
centered,pcaRes-method Class for representing a PCA result
checkData Do some basic checks on a given data matrix
completeObs Class for representing a PCA result
completeObs,pcaRes-method Class for representing a PCA result
dim.pcaRes Class for representing a PCA result
fitted,pcaRes-method Extract fitted values from PCA.
fitted.pcaRes Extract fitted values from PCA.
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
leverage,pcaRes-method Class for representing a PCA result
llsImpute LLSimpute algorithm
loadings.pcaRes Class for representing a PCA result
metaboliteData An incomplete metabolite data set from an Arabidopsis coldstress experiment
metaboliteDataComplete A complete metabolite data set from an Arabidopsis coldstress experiment
method Class for representing a PCA result
method,pcaRes-method Class for representing a PCA result
nipalsPca Perform principal component analysis using the Non-linear iterative partial least squares (NIPALS) algorithm.
nlpca Non-linear PCA
nlpcaNet Class for representing a neural network for computing Non-linear PCA
nlpcaNet-class Class for representing a neural network for computing Non-linear PCA
nni Nearest neighbour imputation
nniRes Class for representing a nearest neighbour imputation result
nniRes-class Class for representing a nearest neighbour imputation result
nObs Class for representing a PCA result
nObs,pcaRes-method Class for representing a PCA result
nPcs Class for representing a PCA result
nPcs,pcaRes-method Class for representing a PCA result
nVar Class for representing a PCA result
nVar,pcaRes-method Class for representing a PCA result
pca Perform principal component analysis
pcaRes Class for representing a PCA result
pcaRes-class Class for representing a PCA result
plotPcs Plot many side by side scores XOR loadings plots
plotR2 R2 plot (screeplot) for PCA
ppca Probabilistic PCA Missing Value Estimator
predict,pcaRes-method Predict values from PCA.
predict.pcaRes Predict values from PCA.
prep Preprocess a matrix for PCA
print,nniRes-method Class for representing a nearest neighbour imputation result
print,pcaRes-method Class for representing a PCA result
Q2 Perform internal cross-validation for PCA
residuals,pcaRes-method Residuals values from a PCA model.
residuals.pcaRes Residuals values from a PCA model.
robustPca PCA implementation based on robustSvd
robustSvd Alternating L1 Singular Value Decomposition
scores.pcaRes Class for representing a PCA result
sDev Class for representing a PCA result
sDev,pcaRes-method Class for representing a PCA result
show,pcaRes-method Class for representing a PCA result
slplot Plot a side by side scores and loadings plot
slplot,pcaRes-method Class for representing a PCA result
summary,pcaRes-method Class for representing a PCA result
svdImpute SVDimpute algorithm
svdPca Perform principal component analysis using singular value decomposition