filteredFit {FRESA.CAD}

A generic pipeline of Feature Selection, Transformation, Scale and fit

Description

Sequential application of feature selection, linear transformation, data scaling then fit

Usage

	
    filteredFit(formula = formula, 
	            data=NULL,
	            filtermethod=univariate_KS,
	            filtermethod.control=list(limit=0),
				Transf=c("none","PCA","CCA","ILAA"),
				Transf.control=list(thr=0.8),
	            Scale="none",
				Scale.control=list(strata=NA),
				refNormIDs=NULL,
				trainIDs=NULL,
	            fitmethod=e1071::svm,
	            ...
	            )

Arguments

formula

the base formula to extract the outcome

data

the data to be used for training the KNN method

filtermethod

the method for feature selection

filtermethod.control

the set of parameters required by the feature selection function

Scale

Scale the data using the provided method

Scale.control

Scale parameters

Transf

Data transformations: "none","PCA","CCA" or "ILAA",

Transf.control

Parameters to the transformation function

fitmethod

The fit function to be used

trainIDs

The list of sample IDs to be used for training

refNormIDs

The list of sample IDs to be used for transformations. ie. Reference Control IDs

...

Parameters for the fitting function

Value

fit

The fitted model

filter

The output of the feature selection function

selectedfeatures

The character vector with all the selected features

usedFeatures

The set of features used for training

parameters

The parameters passed to the fitting method

asFactor

Indicates if the fitting was to a factor

classLen

The number of possible outcomes

Author(s)

Jose G. Tamez-Pena