pcaMethods: A collection of PCA methods

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.

Author
Wolfram Stacklies, Henning Redestig, Kevin Wright
Date of publication
None
Maintainer
Henning Redestig <henning.red@gmail.com>
License
GPL (>= 3)
Version
1.66.0
URLs

View on Bioconductor

Man pages

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...

Files in this package

pcaMethods/COPYING
pcaMethods/DESCRIPTION
pcaMethods/NAMESPACE
pcaMethods/R
pcaMethods/R/AllClasses.R
pcaMethods/R/AllGenerics.R
pcaMethods/R/BPCA_dostep.R
pcaMethods/R/BPCA_initmodel.R
pcaMethods/R/bpca.R
pcaMethods/R/checkData.R
pcaMethods/R/derrorHierarchic.R
pcaMethods/R/errorHierarchic.R
pcaMethods/R/forkNlpcaNet.R
pcaMethods/R/kEstimate.R
pcaMethods/R/kEstimateFast.R
pcaMethods/R/lineSearch.R
pcaMethods/R/llsImpute.R
pcaMethods/R/methods-ExpressionSet.R
pcaMethods/R/methods-nniRes.R
pcaMethods/R/methods-pcaRes.R
pcaMethods/R/nipalsPca.R
pcaMethods/R/nlpca.R
pcaMethods/R/optiAlgCgd.R
pcaMethods/R/orth.R
pcaMethods/R/pca.R
pcaMethods/R/pcaMethods-package.R
pcaMethods/R/ppca.R
pcaMethods/R/prep.R
pcaMethods/R/repmat.R
pcaMethods/R/robustPca.R
pcaMethods/R/sortFeatures.R
pcaMethods/R/svdImpute.R
pcaMethods/R/vector2matrices.R
pcaMethods/R/xval.R
pcaMethods/README.md
pcaMethods/build
pcaMethods/build/vignette.rds
pcaMethods/data
pcaMethods/data/helix.RData
pcaMethods/data/metaboliteData.RData
pcaMethods/data/metaboliteDataComplete.RData
pcaMethods/extra
pcaMethods/extra/missingProblem.R
pcaMethods/inst
pcaMethods/inst/CITATION
pcaMethods/inst/doc
pcaMethods/inst/doc/missingValues.R
pcaMethods/inst/doc/missingValues.Rnw
pcaMethods/inst/doc/missingValues.pdf
pcaMethods/inst/doc/outliers.R
pcaMethods/inst/doc/outliers.Rnw
pcaMethods/inst/doc/outliers.pdf
pcaMethods/inst/doc/pcaMethods.R
pcaMethods/inst/doc/pcaMethods.Rnw
pcaMethods/inst/doc/pcaMethods.pdf
pcaMethods/man
pcaMethods/man/BPCA_dostep.Rd
pcaMethods/man/BPCA_initmodel.Rd
pcaMethods/man/DModX-pcaRes-method.Rd
pcaMethods/man/Q2.Rd
pcaMethods/man/R2VX-pcaRes-method.Rd
pcaMethods/man/R2cum-pcaRes-method.Rd
pcaMethods/man/RnipalsPca.Rd
pcaMethods/man/asExprSet.Rd
pcaMethods/man/biplot-methods.Rd
pcaMethods/man/bpca.Rd
pcaMethods/man/center-pcaRes-method.Rd
pcaMethods/man/centered-pcaRes-method.Rd
pcaMethods/man/checkData.Rd
pcaMethods/man/completeObs-nniRes-method.Rd
pcaMethods/man/cvseg.Rd
pcaMethods/man/cvstat-pcaRes-method.Rd
pcaMethods/man/deletediagonals.Rd
pcaMethods/man/derrorHierarchic.Rd
pcaMethods/man/dim.pcaRes.Rd
pcaMethods/man/errorHierarchic.Rd
pcaMethods/man/fitted-methods.Rd
pcaMethods/man/forkNlpcaNet.Rd
pcaMethods/man/getHierarchicIdx.Rd
pcaMethods/man/helix.Rd
pcaMethods/man/kEstimate.Rd
pcaMethods/man/kEstimateFast.Rd
pcaMethods/man/leverage-pcaRes-method.Rd
pcaMethods/man/lineSearch.Rd
pcaMethods/man/linr.Rd
pcaMethods/man/listPcaMethods.Rd
pcaMethods/man/llsImpute.Rd
pcaMethods/man/loadings-ANY-method.Rd
pcaMethods/man/loadings-pcaRes-method.Rd
pcaMethods/man/loadings.pcaRes.Rd
pcaMethods/man/metaboliteData.Rd
pcaMethods/man/metaboliteDataComplete.Rd
pcaMethods/man/method-pcaRes-method.Rd
pcaMethods/man/nObs-pcaRes-method.Rd
pcaMethods/man/nP-pcaRes-method.Rd
pcaMethods/man/nPcs-pcaRes-method.Rd
pcaMethods/man/nVar-pcaRes-method.Rd
pcaMethods/man/nipalsPca.Rd
pcaMethods/man/nlpca.Rd
pcaMethods/man/nmissing-pcaRes-method.Rd
pcaMethods/man/nni.Rd
pcaMethods/man/nniRes.Rd
pcaMethods/man/optiAlgCgd.Rd
pcaMethods/man/orth.Rd
pcaMethods/man/pca.Rd
pcaMethods/man/pcaMethods-deprecated.Rd
pcaMethods/man/pcaMethods.Rd
pcaMethods/man/pcaNet.Rd
pcaMethods/man/pcaRes.Rd
pcaMethods/man/plot.pcaRes.Rd
pcaMethods/man/plotPcs.Rd
pcaMethods/man/ppca.Rd
pcaMethods/man/predict-methods.Rd
pcaMethods/man/prep.Rd
pcaMethods/man/rediduals-methods.Rd
pcaMethods/man/repmat.Rd
pcaMethods/man/robustPca.Rd
pcaMethods/man/robustSvd.Rd
pcaMethods/man/sDev-pcaRes-method.Rd
pcaMethods/man/scaled-pcaRes-method.Rd
pcaMethods/man/scl-pcaRes-method.Rd
pcaMethods/man/scores-pcaRes-method.Rd
pcaMethods/man/scores.pcaRes.Rd
pcaMethods/man/show-methods.Rd
pcaMethods/man/showNniRes.Rd
pcaMethods/man/simpleEllipse.Rd
pcaMethods/man/slplot-pcaRes-method.Rd
pcaMethods/man/sortFeatures.Rd
pcaMethods/man/summary.Rd
pcaMethods/man/svdImpute.Rd
pcaMethods/man/svdPca.Rd
pcaMethods/man/tempFixNas.Rd
pcaMethods/man/vector2matrices-matrix-method.Rd
pcaMethods/man/vector2matrices-nlpcaNet-method.Rd
pcaMethods/man/wasna-pcaRes-method.Rd
pcaMethods/man/weightsAccount.Rd
pcaMethods/src
pcaMethods/src/RcppExports.cpp
pcaMethods/src/nipals.cpp
pcaMethods/vignettes
pcaMethods/vignettes/missingValues.Rnw
pcaMethods/vignettes/outliers.Rnw
pcaMethods/vignettes/pcaMethods.Rnw