htd.holdout {HEMDAG}

HTD-DAG holdout

Description

Correct the computed scores in a hierarchy according to the HTD-DAG algorithm applying a classical holdout procedure.

Usage

htd.holdout(S, g, testIndex, norm = FALSE, norm.type = NULL)

Arguments

S

a named flat scores matrix with examples on rows and classes on columns.

g

a graph of class graphNEL. It represents the hierarchy of the classes.

testIndex

a vector of integer numbers corresponding to the indexes of the elements (rows) of the scores matrix S to be used in the test set.

norm

a boolean value. Should the flat score matrix be normalized? By default norm=FALSE. If norm=TRUE the matrix S is normalized according to the normalization type selected in norm.type.

norm.type

a string character. It can be one of the following values:

1. NULL (def.): none normalization is applied (norm=FALSE)

2. maxnorm: each score is divided for the maximum value of each class;

3. qnorm: quantile normalization. preprocessCore package is used;

Value

A matrix with the scores of the classes corrected according to the HTD-DAG algorithm. Rows of the matrix are shrunk to testIndex.

Examples

data(graph);
data(scores);
data(test.index);
S.htd <- htd.holdout(S, g, testIndex=test.index, norm=FALSE, norm.type=NULL);