graph2paths: produce list of vectors of (shortest) paths from root to all...

In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

produce list of vectors of (shortest) paths from root to all nodes in gr

Description

produce list of vectors of (shortest) paths from root to all nodes in gr

Usage

graph2paths(gr, root = "http://www.ifomis.org/bfo/1.1#Entity", excise = NULL)

Arguments

gr	graphNEL (package graph) instance representing an ontology
root	character(1) node from which to produce paths
excise	character() or NULL, path steps to exclude

Examples

if (!requireNamespace("graph")) stop("install graph package from Bioconductor to use this function")
jpath = system.file("json", "aut.json.gz", package="ontoProc")
cg = jowl2classgraph(jpath,
  dropstrings = "http://purl.org/autism-ontology/1.0/autism-rules.owl#")
evec = grep("span\\#|snap\\#", graph::nodes(cg), value=TRUE)
paths = graph2paths(cg, excise=evec)
tail(paths)

vjcitn/ontoProc documentation built on July 5, 2025, 6:31 a.m.