Man pages for hredestig/pcaMethods
A collection of PCA methods

asExprSetConvert pcaRes object to an expression set
biplot-methodsPlot a overlaid scores and loadings plot
bpcaBayesian PCA missing value estimation
BPCA_dostepDo BPCA estimation step
BPCA_initmodelInitialize BPCA model
centered-pcaRes-methodCheck centering was part of the model
center-pcaRes-methodGet the centers of the original variables
checkDataDo some basic checks on a given data matrix
completeObs-nniRes-methodGet the original data with missing values replaced with...
cvsegGet CV segments
cvstat-pcaRes-methodGet cross-validation statistics (e.g. Q^2).
deletediagonalsDelete diagonals
dim.pcaResDimensions of a PCA model
fitted-methodsExtract fitted values from PCA.
forkNlpcaNetComplete copy of nlpca net object
getHierarchicIdxIndex in hiearchy
helixA helix structured toy data set
kEstimateEstimate best number of Components for missing value...
kEstimateFastEstimate best number of Components for missing value...
leverage-pcaRes-methodExtract leverages of a PCA model
lineSearchLine search for conjugate gradient
linrLinear kernel
listPcaMethodsList PCA methods
llsImputeLLSimpute algorithm
loadings-ANY-methodCrude way to unmask the function with the same name from...
loadings.pcaResGet loadings from a pcaRes object
loadings-pcaRes-methodGet loadings from a pcaRes object
metaboliteDataA incomplete metabolite data set from an Arabidopsis...
metaboliteDataCompleteA complete metabolite data set from an Arabidopsis coldstress...
method-pcaRes-methodGet the used PCA method
nlpcaNon-linear PCA
nmissing-pcaRes-methodMissing values
nniNearest neighbour imputation
nniResClass for representing a nearest neighbour imputation result
nObs-pcaRes-methodGet the number of observations used to build the PCA model.
nPcs-pcaRes-methodGet number of PCs.
nP-pcaRes-methodGet number of PCs
nVar-pcaRes-methodGet the number of variables used to build the PCA model.
optiAlgCgdConjugate gradient optimization
orthCalculate an orthonormal basis
pcaPerform principal component analysis
pcaMethods-deprecatedDeprecated methods for pcaMethods
pcaNetClass representation of the NLPCA neural net
pcaResClass for representing a PCA result
plot.pcaResPlot diagnostics (screeplot)
plotPcsPlot many side by side scores XOR loadings plots
ppcaProbabilistic PCA
predict-methodsPredict values from PCA.
prepPre-process a matrix for PCA
Q2Cross-validation for PCA
R2cum-pcaRes-methodCumulative R2 is the total ratio of variance that is being...
R2VX-pcaRes-methodR2 goodness of fit
rediduals-methodsResiduals values from a PCA model.
repmatReplicate and tile an array.
RnipalsPcaNIPALS PCA implemented in R
robustPcaPCA implementation based on robustSvd
robustSvdAlternating L1 Singular Value Decomposition
scaled-pcaRes-methodCheck if scaling was part of the PCA model
scl-pcaRes-methodGet the scales (e.g. standard deviations) of the original...
scores.pcaResGet scores from a pcaRes object
scores-pcaRes-methodGet scores from a pcaRes object
sDev-pcaRes-methodGet the standard deviations of the scores (indicates their...
show-methodsPrint/Show for pcaRes
showNniResPrint a nniRes model
simpleEllipseHotelling's T^2 Ellipse
slplot-pcaRes-methodSide by side scores and loadings plot
sortFeaturesSort the features of NLPCA object
summarySummary of PCA model
svdImputeSVDimpute algorithm
svdPcaPerform principal component analysis using singular value...
tempFixNasTemporary fix for missing values
vector2matrices-matrix-methodTranform the vectors of weights to matrix structure
vector2matrices-nlpcaNet-methodTranform the vectors of weights to matrix structure
wasna-pcaRes-methodGet a matrix with indicating the elements that were missing...
weightsAccountCreate an object that holds the weights for nlpcaNet. Holds...
hredestig/pcaMethods documentation built on Nov. 6, 2019, 3:27 p.m.