HEMDAG (version 2.6.1)

full.annotation.matrix: Full annotation matrix

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.

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 \(j\).

Details

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

See Also

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

Examples

# NOT RUN {
data(wadj);
data(graph);
data(labels);
anc <- build.ancestors(g);
full.ann <- full.annotation.matrix(W, anc, L);
# }