obo2graphNEL: convert a typical OBO text file to a graphNEL instance (using...

In gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Description

convert a typical OBO text file to a graphNEL instance (using Term elements)

Usage

obo2graphNEL(
  obo = "human-phenotype-ontology.obo",
  kill = "\\[Typedef\\]",
  killTrailSp = TRUE
)

Arguments

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.

Details

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.

Value

a graphNEL instance

Note

The OBO for Human Disease ontology is serialized as text with this package.

Author(s)

VJ Carey <[e-mail]>

References

For use with human disease ontology, http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease_ontology

Examples

data(efo.obo.g)
requireNamespace("graph")
hn = graph::nodes(efo.obo.g)[1:5]
hn
graph::nodeData(efo.obo.g, hn[5])

gwascat documentation built on Nov. 8, 2020, 11:08 p.m.