Create a spls.constraint object by fitting a constraint spls on a bootsPLS object

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Description

Create a spls.constraint object by fitting a constraint spls with the spls.hybrid function on a ‘bootsPLS’ object

Usage

1
fit.model(object,auto.tune,X,Y,ncomp,keepX.constraint,alpha,limit)

Arguments

object

a ‘spls.constraint’ object', as obtained from bootsPLS.

auto.tune

Logical. If TRUE, tune the optimal number of component (ncomp) and which variables to select on each component (keepX.constraint). It only works with object

X

Input matrix of dimension n * p; each row is an observation vector.

Y

Factor with at least q>2 levels.

ncomp

How many component are to be included in the sPLS-DA analysis?

keepX.constraint

A list containing which variables to keep on each component.

alpha

Level of the test.

limit

Vector of maximal number of genes to include on each component.

Details

This function fit a spls.hybrid on the variables included in keepX.constraint, which can be an input or internally calculated by setting auto.tune=TRUE. If object is given as an input, (X, Y) are ignored. If auto.tune=TRUE, (ncomp, keepX.constraint) are ignored.

Value

A 'spls.constraint' object is returned for which plotIndiv is available.

The outputs are the ones from spls.hybrid, plus

data

A list of the input data X, Y, Y.mat (dummy matrix) and of keepX.constraint, which is a list containing the variables kept on each component.

See Also

prediction, CI.prediction, plotIndiv

Examples

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## Not run: 
data(MSC)
X=MSC$X
Y=MSC$Y


boot=bootsPLS(X=X,Y=Y,ncomp=3,many=5,kCV=5)

# with a bootsPLS object and auto.tune=TRUE
fit=fit.model(boot,auto.tune=TRUE)

# with a bootsPLS object and ncomp=2
fit=fit.model(boot,ncomp=2)

# with a bootsPLS object and ncomp/keepX.constraint as input
keepX.constraint=fit$data$keepX.constraint
fit=fit.model(boot,ncomp=2,keepX.constraint=keepX.constraint)

# with no bootsPLS object
fit=fit.model(X=X,Y=Y,ncomp=2,keepX.constraint=keepX.constraint)# bootsPLS object

plotIndiv(fit,ind.names=FALSE,col=as.numeric(Y))


## End(Not run)