full.annotation.matrix: Full annotation matrix

In HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

Description

Build a full annotations matrix using the ancestor list and the most specific annotations matrix w.r.t. a given weighted adjacency matrix (wadj). The rows of the full annotation matrix correspond to all the examples of the given weighted adjacency matrix and the columns to the class/terms. The transitive closure of the annotations is performed.

Usage

full.annotation.matrix(W, anc, ann.spec)

Arguments

W	a symmetric adjacency weighted matrix of the graph.
anc	the ancestor list.
ann.spec	the annotation matrix of the most specific annotations (0/1): rows are genes and columns are terms.

Details

The examples present in the annotation matrix (ann.spec) but not in the adjacency weighted matrix (W) are purged.

Value

A full annotation table T, that is a matrix where the transitive closure of annotations is performed. Rows correspond to genes of the weighted adjacency matrix and columns to terms. T[i,j]=1 means that gene i is annotated for the term j, T[i,j]=0 means that gene i is not annotated for the term j.

Examples

data(wadj);
data(graph);
data(labels);
anc <- build.ancestors(g);
full.ann <- full.annotation.matrix(W, anc, L);

HEMDAG documentation built on Feb. 12, 2021, 5:13 p.m.