transitive.closure.annotations: Transitive closure of annotations

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

Description

Performs the transitive closure of the annotations using ancestors and the most specific annotation table. The annotations are propagated from bottom to top, enriching the most specific annotations table. The rows of the matrix correspond to the genes of the most specific annotation table and the columns to the OBO terms/classes.

Usage

transitive.closure.annotations(ann.spec, anc)

Arguments

ann.spec	the annotation matrix of the most specific annotations (0/1): rows are genes and columns are OBO terms.
anc	list of the ancestors of the ontology.

Value

an annotation table T: rows correspond to genes and columns to OBO 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

specific.annotation.matrix, build.ancestors

Examples

data(graph);
data(labels);
anc <- build.ancestors(g);
tca <- transitive.closure.annotations(L, anc);

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