obozinski.methods {HEMDAG}

Obozinski's heuristic methods calling

Description

Compute the Obozinski's heuristic methods Max, And, Or (Obozinski et al., Genome Biology, 2008).

Usage

obozinski.methods(S, g, heuristic = "and", 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.

heuristic

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

1. "max": run the method obozinski.max;

2. "and": run the method obozinski.and;

3. "or": run the method obozinski.or;

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 chosen heuristic algorithm.

Examples

data(graph);
data(scores);
S.and <- obozinski.methods(S, g, heuristic="and", norm=TRUE, norm.type="maxnorm");