A collection of PCA methods.


[Package List] [Top]

Documentation for package ‘pcaMethods’ version 1.14.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

asExprSet Convert pcaRes object to an expression set
bpca Bayesian PCA Missing Value Estimator
checkData Do some basic checks on a given data matrix
completeObs,pcaRes-method 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
llsImpute LLSimpute algorithm
metaboliteData An incomplete metabolite data set from an Arabidopsis coldstress experiment
metaboliteDataComplete A complete metabolite data set from an Arabidopsis coldstress experiment
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
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
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
robustPca PCA implementation based on robustSvd
robustSvd Alternating L1 Singular Value Decomposition
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