Human Phenotype Phenotypic Abnormality (HPPA).

Description

An R object that contains information on Human Phenotype Phenotypic Abnormality terms. These terms are organised as a direct acyclic graph (DAG), which is further stored as an object of the class 'igraph' (see http://igraph.org/r/doc/aaa-igraph-package.html). This data is prepared based on http://purl.obolibrary.org/obo/hp.obo.

Usage

data(ig.HPPA)

Value

an object of class "igraph". As a direct graph, it has attributes to vertices/nodes and edges:

  • vertex attributes: "name" (i.e. "Term ID"), "term_id" (i.e. "Term ID"), "term_name" (i.e "Term Name") and "term_distance" (i.e. Term Distance: the distance to the root; always 0 for the root itself)
  • edge attributes: "relation" (either 'is_a' or 'part_of')

References

Robinson et al. (2012) The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet, 83:610-615.

Examples

ig.HPPA <- dRDataLoader(RData='ig.HPPA')
'ig.HPPA' (from package 'dnet' version 1.0.11) has been loaded into the working environment (at 2017-03-27 19:59:09)
ig.HPPA
IGRAPH DN-- 11389 15221 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (vertex names): [1] HP:0000002->HP:0000098 HP:0000002->HP:0004322 HP:0000002->HP:0012772 [4] HP:0000008->HP:0000130 HP:0000008->HP:0000137 HP:0000008->HP:0000140 [7] HP:0000008->HP:0000142 HP:0000008->HP:0011027 HP:0000009->HP:0000011 [10] HP:0000009->HP:0000012 HP:0000009->HP:0000016 HP:0000009->HP:0000017 [13] HP:0000009->HP:0000019 HP:0000009->HP:0000020 HP:0000009->HP:0000076 [16] HP:0000009->HP:0000805 HP:0000009->HP:0002839 HP:0000009->HP:0005340 [19] HP:0000009->HP:0100515 HP:0000009->HP:0100518 HP:0000010->HP:0012786 + ... omitted several edges