Human Phenotype Clinical Modifier (HPCM).

Description

An R object that contains information on Human Phenotype Clinical Modifier 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.HPCM <- dRDataLoader(RData = "ig.HPCM")

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.HPCM <- dRDataLoader(RData='ig.HPCM')
'ig.HPCM' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.HPCM.RData?raw=true) has been loaded into the working environment (at 2017-03-27 19:59:05)
ig.HPCM
IGRAPH DN-- 53 52 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (vertex names): [1] HP:0003577->HP:0011460 HP:0003577->HP:0011461 HP:0003581->HP:0003584 [4] HP:0003581->HP:0003596 HP:0003581->HP:0011462 HP:0003674->HP:0003577 [7] HP:0003674->HP:0003581 HP:0003674->HP:0003593 HP:0003674->HP:0003621 [10] HP:0003674->HP:0003623 HP:0003674->HP:0011463 HP:0003679->HP:0003676 [13] HP:0003679->HP:0003677 HP:0003679->HP:0003678 HP:0003679->HP:0003680 [16] HP:0003679->HP:0003682 HP:0003812->HP:0003828 HP:0003812->HP:0003829 [19] HP:0003829->HP:0003831 HP:0011008->HP:0003587 HP:0011008->HP:0011009 + ... omitted several edges