build.edges.from.hpo.obo: Parse an HPO obo file

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

Parse an HPO obo file

Description

Read an HPO obo file (HPO) 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 vertexes separated by blank.

Usage

build.edges.from.hpo.obo(obofile = "hp.obo", file = "edge.file")

Arguments

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

Details

A faster and more flexible parser to handle obo file can be found here.

Value

A text file representing the edges in the format: source destination (i.e. one row for each edge).

Examples

## Not run: 
hpobo <- "http://purl.obolibrary.org/obo/hp.obo";
build.edges.from.hpo.obo(obofile=hpobo, file="hp.edge");
## End(Not run)

AnacletoLAB/HEMDAG documentation built on Oct. 14, 2022, 9:18 p.m.