A collection of PCA methods.


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Documentation for package ‘pcaMethods’ version 1.36.0

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A B C D E F G H K L M N O P Q R S T V W

-- A --

asExprSet Convert pcaRes object to an expression set

-- B --

biplot-method Biplot for pcaRes method.
biplot.pcaRes Plot a overlaid scores and loadings plot
bpca Bayesian PCA Missing Value Estimator
BPCA_dostep Do BPCA estimation step
BPCA_initmodel Initialize BPCA model

-- C --

center Get the centers of the original variables...
center-method Get the centers of the original variables...
centered Check centering was part of the model...
centered-method Check centering was part of the model...
checkData Do some basic checks on a given data matrix
completeObs Get the original data with missing values replaced with predicted...
completeObs-method Get the original data with missing values replaced with predicted...
cvstat Get cross-validation statistics (e...
cvstat-method Get cross-validation statistics (e...

-- D --

deletediagonals Delete diagonals
derrorHierarchic Later...
dim.pcaRes Dimensions of a PCA model...
DModX DModX
DModX-method DModX

-- E --

errorHierarchic Later...

-- F --

fitted-method Fitted PCA data.
fitted.pcaRes Extract fitted values from PCA.
forkNlpcaNet Complete copy of nlpca net object...

-- G --

getHierarchicIdx Index in hiearchy...

-- H --

helix A helix structured toy data set

-- K --

kEstimate Estimate best number of Components for missing value estimation
kEstimateFast Estimate best number of Components for missing value estimation

-- L --

leverage Extract leverages of a PCA model
leverage-method Extract leverages of a PCA model
lineSearch Line search for conjugate gradient...
linr Linear kernel...
listPcaMethods List PCA methods
llsImpute LLSimpute algorithm
loadings.pcaRes Get the loadings from a PCA model...

-- M --

metaboliteData A incomplete metabolite data set from an Arabidopsis coldstress experiment
metaboliteDataComplete A complete metabolite data set from an Arabidopsis coldstress experiment
method Get the used PCA method...
method-method Get the used PCA method...

-- N --

nFit Class representation of the NLPCA neural net
nFit-class Class representation of the NLPCA neural net
nipalsPca NIPALS PCA
nlpca Non-linear PCA
nlpcaNet Class representation of the NLPCA neural net
nlpcaNet-class Class representation of the NLPCA neural net
nmissing Missing values...
nmissing-method Missing values...
nni Nearest neighbour imputation
nniRes Class for representing a nearest neighbour imputation result
nniRes-class Class for representing a nearest neighbour imputation result
nObs Get the number of observations used to build the PCA model.
nObs-method Get the number of observations used to build the PCA model.
nP Get number of PCs...
nP-method Get number of PCs...
nPcs Get number of PCs.
nPcs-method Get number of PCs.
nVar Get the number of variables used to build the PCA model.
nVar-method Get the number of variables used to build the PCA model.

-- O --

optiAlgCgd Conjugate gradient optimization...
orth Calculate an orthonormal basis

-- P --

pca Perform principal component analysis
pcaMethods pcaMethods
pcaMethods-deprecated Deprecated methods for pcaMethods
pcaRes Class for representing a PCA result
pcaRes-class Class for representing a PCA result
plot.pcaRes Plot diagnostics (screeplot)
plotPcs Plot many side by side scores XOR loadings plots
plotR2 R2 plot (screeplot) for PCA
ppca Probabilistic PCA
predict-method Predict PCA data.
predict.pcaRes Predict values from PCA.
prep Pre-process a matrix for PCA
print-method Print basic info...

-- Q --

Q2 Cross-validation for PCA

-- R --

R2cum Cumulative R2 is the total ratio of variance that is being...
R2cum-method Cumulative R2 is the total ratio of variance that is being...
repmat Replicate and tile an array.
resid-method Residuals of PCA data.
residuals-method Residuals of PCA data.
residuals.pcaRes Residuals values from a PCA model.
RnipalsPca NIPALS PCA implemented in R
robustPca PCA implementation based on robustSvd
robustSvd Alternating L1 Singular Value Decomposition

-- S --

scaled Check if scaling was part of the PCA model...
scaled-method Check if scaling was part of the PCA model...
scl Get the scales (e...
scl-method Get the scales (e...
scores.pcaRes Get the scores from a PCA model...
sDev Get the standard deviations of the scores (indicates their...
sDev-method Get the standard deviations of the scores (indicates their...
show-method Show pcaRes / nniRes objects.
showNniRes Print a nniRes model
showPcaRes Print/Show for pcaRes
simpleEllipse Hotelling's T^2 Ellipse
slplot Side by side scores and loadings plot
slplot-method Side by side scores and loadings plot
sortFeatures Sort the features of NLPCA object...
summary Summary of PCA model
summary-method Summary of PCA model
svdImpute SVDimpute algorithm
svdPca Perform principal component analysis using singular value decomposition

-- T --

tempFixNas Temporary fix for missing values

-- V --

vector2matrices-method Tranform the vectors of weights to matrix structure...

-- W --

wasna Get a matrix with indicating the elements that were missing in the...
wasna-method Get a matrix with indicating the elements that were missing in the...
weightsAccount Create an object that holds the weights for nlpcaNet.