Human Phenotype Mode of Inheritance (HPMI).

Description

An R object that contains information on Human Phenotype Mode of Inheritance 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

ig.HPMI <- dRDataLoader(RData = "ig.HPMI")

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.HPMI <- dRDataLoader(RData='ig.HPMI')
'ig.HPMI' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.HPMI.RData?raw=true) has been loaded into the working environment (at 2017-03-27 19:59:09)
ig.HPMI
IGRAPH DN-- 27 27 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (vertex names): [1] HP:0000005->HP:0000006 HP:0000005->HP:0000007 HP:0000005->HP:0001425 [4] HP:0000005->HP:0001426 HP:0000005->HP:0001427 HP:0000005->HP:0001428 [7] HP:0000005->HP:0001466 HP:0000005->HP:0001472 HP:0000005->HP:0003743 [10] HP:0000005->HP:0003745 HP:0000005->HP:0010985 HP:0000006->HP:0001444 [13] HP:0000006->HP:0001452 HP:0000006->HP:0001470 HP:0000006->HP:0012274 [16] HP:0000006->HP:0012275 HP:0001417->HP:0001419 HP:0001417->HP:0001423 [19] HP:0001426->HP:0010982 HP:0001426->HP:0010983 HP:0001426->HP:0010984 + ... omitted several edges