opls: Orthogonal Projections to Latent Structures (OPLS) for a...

In ricoderks/Rcpm: General functions for the Center of Proteomics and Metabolomics (LUMC)

Orthogonal Projections to Latent Structures (OPLS) for a single Y

Description

Orthogonal Projections to Latent Structures (OPLS) for a single Y. Written by E.Nevedomskaya 2007-2013. Based on malab script by O. Cloarec Imperial College, London.

Usage

opls(Xi, Yi, prep, A, ncox, ncoy, nrcv)

Arguments

Xi	X matrix input
Yi	Y column input
prep	preprocessing, "no", no preprocessing, "mc" mean centering, "uv" univariance scaling
A	number of correlated components, it can be determinated by PCA of Y'X
ncox	number of orthogonal components in X
ncoy	number of orthogonal component in Y
nrcv	number of fold in the cross-validation (full cross validation)

Details

Orthogonal Projections to Latent Structures (OPLS) for a single Y. The number of components can be determined with the function ncomp_opls.

Value

Output is a list with the following elements:

MeanX	variable means for the X table
MeanY	variable means for the Y table
VarX	variance of the variables in the X table
VarY	variance of the variables in the Y table
svd	results of the SVD transformation of the X-Y covariance table
T	T scores
Ts	X scores
E	residuals
wo	Y-orthogonal loadings (non-normalized)
TYosc	orthogonal scores
PYosc	Y-orthogonal loadings
Wosc	orthogonal weights
R2Xyo	modelled percentage of X orthogonal to Y
R2Xcorr	modelled percentage of X correlated to Y
R2XcorrVar	modelled percentage of X variance correlated to Y
R2X	total percentage of X that had been modelled
U	U scores
F	residuals
R2Ycorr	modelled percentage of Y correlated to X
R2Y	total percentage of X that had been modelled
P	loadings
Bu	regression coefficients
Bt	regression coefficients
Yhat	Y predicted by the regression
R2Yhat	predicted by the regression variance of Y
R2Yhatcum	cumulative predicted (by the regression) variance of Y
R2Xhat	predicted (by the regression) variance of X
R2Xhatcum	cumulative predicted variance of X
Tcv	cross-validated T-scores
TYosccv	cross-validated Y-orthogonal scores
Ucv	cross-validated T-scores
YPRESSf	cumulative predicted residual sums of squares (PRESS) of Y
YPRESSi	PRESS for each column of Y
XPRESSf	cumulative predicted residual sums of squares (PRESS) of X
XPRESSi	PRESS for each column of X
Yhatcv	Y predicted in cross-validation (CV)
Xhatcv	X predicted in cross-validation
Q2Yhatcum	cumulative predicted in CV variance of Y
Q2Yhat	variance of Y predicted in CV
Q2Xhatcum	cumulative predicted in CV variance of X
Q2Xhat	variance of Y predicted in CV

Author(s)

E. Nevedomskaya

Rico Derks

ricoderks/Rcpm documentation built on May 18, 2022, 7:49 a.m.