full.annotation.matrix: Full annotation matrix

In gecko515/HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

Description

Construct a full annotations table using ancestors and the most specific annotations table 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	symmetric adjacency weighted matrix of the graph.
anc	list of the ancestors of the ontology.
ann.spec	the annotation matrix of the most specific annotations (0/1): rows are genes and columns are classes.

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 in which the transitive closure of annotations was 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.

See Also

weighted.adjacency.matrix, build.ancestors,
specific.annotation.matrix, transitive.closure.annotations

Examples

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

gecko515/HEMDAG documentation built on Oct. 18, 2019, 6:34 a.m.