dag_funcs: GAPGOM internal - Directed acyclic graph (DAG) mathematical...

In Berghopper/GAPGOM: GAPGOM (novel Gene Annotation Prediction and other GO Metrics)

Description

These functions are internal functions and should not be called by the user.

Usage

.common_ancestors(go_id1, go_id2, ontology, organism, go_annotation,
  information_content)

.set_edge_weight(sub_graph, information_content)

.longest_path(weighted_dag, go_annotation, last_common_ancestor, root,
  information_content)

.get_last_common_ancestors(go1, go2, ontology, organism, root,
  go_annotation, information_content)

.get_short_path_info(go_id, last_common_ancestor, weighted_graph,
  go_annotation, information_content)

.find_disjunctive_lcas(lcas, topoargs)

.all_go_similarities(all_go_pairs_df, topoargs, drop = NULL)

Details

Mathematical calculations and navigations functions for directed acyclic graphs (DAG). These functions do a multitude of things; calculate longest paths between two nodes, calculate edge weight and retrieving a common ancestor in the GO DAG given two GO ids.

Value

output is different on a case-to-case basis

Notes

Internal functions all used in topo_ic_sim_titj().

Berghopper/GAPGOM documentation built on July 2, 2020, 11:57 p.m.