gpav.vanilla {HEMDAG}

GPAV vanilla

Description

Correct the computed scores in a hierarchy according to the GPAV algorithm.

Usage

gpav.vanilla(
  S,
  g,
  W = NULL,
  parallel = FALSE,
  ncores = 1,
  norm = FALSE,
  norm.type = NULL
)

Arguments

S

a named flat scores matrix with examples on rows and classes on columns (root node included).

g

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

W

vector of weight relative to a single example. If W=NULL (def.) it is assumed that W is a unitary vector of the same length of the columns' number of the matrix S (root node included).

parallel

a boolean value. Should the parallel version GPAV be run?

• TRUE: execute the parallel implementation of GPAV (gpav.parallel);

• FALSE (def.): execute the sequential implementation of GPAV (gpav.over.examples);

ncores

number of cores to use for parallel execution. Set ncores=1 if parallel=FALSE, otherwise set ncores to the desired number of cores.

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 named matrix with the scores of the classes corrected according to the GPAV algorithm.

Examples

data(graph);
data(scores);
S.gpav <- gpav.vanilla(S, g, W=NULL, parallel=FALSE, ncores=1, norm=FALSE, norm.type=NULL);