obo2graphNEL {gwascat} | R Documentation |
convert a typical OBO text file to a graphNEL instance (using Term elements)
obo2graphNEL( obo = "human-phenotype-ontology.obo", kill = "\\[Typedef\\]", killTrailSp = TRUE )
obo |
string naming a file in OBO format |
kill |
entity types to be excluded from processing – probably this should be in a 'keep' form, but for now this works. |
killTrailSp |
In the textual version of EFO ca. Aug 2015, there is a trailing blank in the tag field defining EFO:0000001, which is not present in references to this term. Set this to TRUE to eliminate this, or graphNEL construction will fail to validate. |
Very rudimentary list and grep operations are used to retain sufficient information to map the DAG to a graphNEL, using formal term identifiers as node names and 'is-a' relationships as edges, and term names and other metadata are assigned to nodeData components.
a graphNEL instance
The OBO for Human Disease ontology is serialized as text with this package.
VJ Carey <stvjc@channing.harvard.edu>
For use with human disease ontology, http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease_ontology
data(efo.obo.g) requireNamespace("graph") hn = graph::nodes(efo.obo.g)[1:5] hn graph::nodeData(efo.obo.g, hn[5])