Omics Data Integration Project

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Documentation for package ‘mixOmics’ version 3.0

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B C E I J L M N P Q R S U V Y

-- B --

bin.color Internal Functions
breast.tumors Human Breast Tumors Data

-- C --

cim Clustered Image Maps (CIMs) ("heat maps")
cim.default Clustered Image Maps (CIMs) ("heat maps")
cim.pls Clustered Image Maps (CIMs) ("heat maps")
cim.rcc Clustered Image Maps (CIMs) ("heat maps")
cim.spls Clustered Image Maps (CIMs) ("heat maps")

-- E --

estim.regul Estimate the parameters of regularization for Regularized CCA
estim.regul.default Estimate the parameters of regularization for Regularized CCA

-- I --

ica.def Internal Functions
ica.par Internal Functions
image.estim.regul Plot the cross-validation score.
imgCor Image Maps of Correlation Matrices between two Data Sets
ipca Independent Principal Component Analysis

-- J --

jet.colors Jet Colors Palette

-- L --

linnerud Linnerud Dataset
liver.toxicity Liver Toxicity Data
loo Internal Functions

-- M --

map Internal Functions
mat.rank Matrix Rank
Mfold Internal Functions
multidrug Multidrug Resistence Data

-- N --

nearZeroVar Identification of zero- or near-zero variance predictors
network Relevance Network for (r)CCA and (s)PLS regression
network.default Relevance Network for (r)CCA and (s)PLS regression
network.pls Relevance Network for (r)CCA and (s)PLS regression
network.rcc Relevance Network for (r)CCA and (s)PLS regression
network.spls Relevance Network for (r)CCA and (s)PLS regression
nipals Non-linear Iterative Partial Least Squares (NIPALS) algorithm
nutrimouse Nutrimouse Dataset

-- P --

pca Principal Components Analysis
pcasvd Internal Functions
pcatune Tune the number of principal components in PCA
plot.rcc Canonical Correlations Plot
plot.valid Validation Plot
plot3dIndiv Plot of Individuals (Experimental Units) in three dimensions
plot3dIndiv.pca Plot of Individuals (Experimental Units) in three dimensions
plot3dIndiv.pls Plot of Individuals (Experimental Units) in three dimensions
plot3dIndiv.plsda Plot of Individuals (Experimental Units) in three dimensions
plot3dIndiv.rcc Plot of Individuals (Experimental Units) in three dimensions
plot3dIndiv.spca Plot of Individuals (Experimental Units) in three dimensions
plot3dIndiv.spls Plot of Individuals (Experimental Units) in three dimensions
plot3dIndiv.splsda Plot of Individuals (Experimental Units) in three dimensions
plot3dVar Plot of Variables in three dimensions
plot3dVar.pca Plot of Variables in three dimensions
plot3dVar.pls Plot of Variables in three dimensions
plot3dVar.plsda Plot of Variables in three dimensions
plot3dVar.rcc Plot of Variables in three dimensions
plot3dVar.spca Plot of Variables in three dimensions
plot3dVar.spls Plot of Variables in three dimensions
plot3dVar.splsda Plot of Variables in three dimensions
plotIndiv Plot of Individuals (Experimental Units)
plotIndiv.pca Plot of Individuals (Experimental Units)
plotIndiv.pls Plot of Individuals (Experimental Units)
plotIndiv.plsda Plot of Individuals (Experimental Units)
plotIndiv.rcc Plot of Individuals (Experimental Units)
plotIndiv.spca Plot of Individuals (Experimental Units)
plotIndiv.spls Plot of Individuals (Experimental Units)
plotIndiv.splsda Plot of Individuals (Experimental Units)
plotVar Plot of Variables
plotVar.pca Plot of Variables
plotVar.pls Plot of Variables
plotVar.plsda Plot of Variables
plotVar.rcc Plot of Variables
plotVar.spca Plot of Variables
plotVar.spls Plot of Variables
plotVar.splsda Plot of Variables
pls Partial Least Squares (PLS) Regression
plsda Partial Least Squares Discriminate Analysis (PLS-DA).
predict.pls Predict Method for PLS, sPLS, PLS-DA or sPLS-DA
predict.plsda Predict Method for PLS, sPLS, PLS-DA or sPLS-DA
predict.spls Predict Method for PLS, sPLS, PLS-DA or sPLS-DA
predict.splsda Predict Method for PLS, sPLS, PLS-DA or sPLS-DA
print Print Methods for CCA, (s)PLS and Summary objects
print.pca Print Methods for CCA, (s)PLS and Summary objects
print.pls Print Methods for CCA, (s)PLS and Summary objects
print.rcc Print Methods for CCA, (s)PLS and Summary objects
print.spca Print Methods for CCA, (s)PLS and Summary objects
print.spls Print Methods for CCA, (s)PLS and Summary objects
print.summary Print Methods for CCA, (s)PLS and Summary objects
prostate Human Prostate Tumors Data

-- Q --

q2.pls Internal Functions
q2.spls Internal Functions

-- R --

rcc Regularized Canonical Correlation Analysis
rcc.default Regularized Canonical Correlation Analysis

-- S --

s.match Plot of Paired Coordinates
scatterutil.base Graphical utility functions from ade4
scatterutil.eti Graphical utility functions from ade4
scatterutil.grid Graphical utility functions from ade4
sipca Independent Principal Component Analysis
spca Sparse Principal Components Analysis
spls Sparse Partial Least Squares (sPLS)
splsda Sparse Partial Least Squares Discriminate Analysis (sPLS-DA)
srbct Small version of the small round blue cell tumors of childhood data
summary Summary Methods for CCA and PLS objects
summary.pls Summary Methods for CCA and PLS objects
summary.rcc Summary Methods for CCA and PLS objects
summary.spls Summary Methods for CCA and PLS objects

-- U --

unmap Internal Functions

-- V --

valid Compute validation criterion for PLS, sPLS, PLS-DA and sPLS-DA
vip Variable Importance in the Projection (VIP)

-- Y --

yeast Yeast metabolomic study