do.edges.from.HPO.obo

an HPO OBO file. The extension of the obofile can be or plain format (".txt") or compressed (".gz").

obofile

name of the file of the edges to be written.
The extension of the file can be or plain format (".txt") or compressed (".gz").

file

Read an HPO OBO file (<a href="http://human-phenotype-ontology.github.io/">HPO</a>) and write 
the edges of the DAG on a plain text file. The format of the file is a sequence of
rows and each row corresponds to an edge represented through a pair of vertices separated by blanks.

An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).

Marco Notaro

HEMDAG

Hierarchical Ensemble Methods for Directed Acyclic Graphs

Alessandro Petrini

Giorgio Valentini

do.edges.from.HPO.obo function

Read an HPO OBO file (<a href='http://human-phenotype-ontology.github.io/'>HPO</a>) and write 
the edges of the DAG on a plain text file. The format of the file is a sequence of
rows and each row corresponds to an edge represented through a pair of vertices separated by blanks.

do.edges.from.HPO.obo: Parse an HPO OBO file

Description

Usage

Arguments

Value

Details

Examples