filteredFit: 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,
	            ...
	            )

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

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

Author

Jose G. Tamez-Pena