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.

AuthorWolfram Stacklies, Henning Redestig, Kevin Wright
Date of publicationNone
MaintainerHenning Redestig <henning.red@gmail.com>
LicenseGPL (>= 3)
Version1.66.0
https://github.com/hredestig/pcamethods

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...

Functions

asExprSet Man page
biplot-methods Man page
biplot.pcaRes Man page
biplot,pcaRes-method Man page
bpca Man page
BPCA_dostep Man page
BPCA_initmodel Man page
center Man page
centered Man page
centered,pcaRes-method Man page
center,pcaRes-method Man page
checkData Man page
completeObs Man page
completeObs,nniRes-method Man page
completeObs,pcaRes-method Man page
cvseg Man page
cvstat Man page
cvstat,pcaRes-method Man page
deletediagonals Man page
derrorHierarchic Man page
dim.pcaRes Man page
DModX Man page
DModX,pcaRes-method Man page
errorHierarchic Man page
fitted-methods Man page
fitted.pcaRes Man page
fitted,pcaRes-method Man page
forkNlpcaNet Man page
getHierarchicIdx Man page
helix Man page
kEstimate Man page
kEstimateFast Man page
leverage Man page
leverage,pcaRes-method Man page
lineSearch Man page
linr Man page
listPcaMethods Man page
llsImpute Man page
loadings Man page
loadings,ANY-method Man page
loadings.pcaRes Man page
loadings,pcaRes-method Man page
metaboliteData Man page
metaboliteDataComplete Man page
method Man page
method,pcaRes-method Man page
nipalsPca Man page
nlpca Man page
nlpcaNet Man page
nlpcaNet-class Man page
nmissing Man page
nmissing,nniRes-method Man page
nmissing,pcaRes-method Man page
nni Man page
nniRes Man page
nniRes-class Man page
nObs Man page
nObs,pcaRes-method Man page
nP Man page
nPcs Man page
nPcs,pcaRes-method Man page
nP,pcaRes-method Man page
nVar Man page
nVar,pcaRes-method Man page
optiAlgCgd Man page
orth Man page
pca Man page
pcaMethods Man page
pcaMethods-deprecated Man page
pcaMethods-package Man page
pcaNet Man page
pcaRes Man page
pcaRes-class Man page
plot.pcaRes Man page
plot,pcaRes-method Man page
plotPcs Man page
ppca Man page
predict-methods Man page
predict.pcaRes Man page
predict,pcaRes-method Man page
prep Man page
print,nniRes-method Man page
print,pcaRes-method Man page
Q2 Man page
R2cum Man page
R2cum,pcaRes-method Man page
R2VX Man page
R2VX,pcaRes-method Man page
rediduals-methods Man page
repmat Man page
resid,pcaRes-method Man page
residuals.pcaRes Man page
residuals,pcaRes-method Man page
RnipalsPca Man page
robustPca Man page
robustSvd Man page
scaled Man page
scaled,pcaRes-method Man page
scl Man page
scl,pcaRes-method Man page
scores Man page
scores.pcaRes Man page
scores,pcaRes-method Man page
sDev Man page
sDev,pcaRes-method Man page
show-methods Man page
showNniRes Man page
show,nniRes-method Man page
showPcaRes Man page
show,pcaRes-method Man page
simpleEllipse Man page
slplot Man page
slplot,pcaRes-method Man page
sortFeatures Man page
summary Man page
summary.pcaRes Man page
summary,pcaRes-method Man page
svdImpute Man page
svdPca Man page
tempFixNas Man page
vector2matrices,matrix-method Man page
vector2matrices,nlpcaNet-method Man page
wasna Man page
wasna,pcaRes-method Man page
weightsAccount Man page

Files

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

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