| full.annotation.matrix {HEMDAG} | R Documentation |
Full annotation matrix
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);