Mammalian Phenotype (MP).

Description

An R object that contains information on Mammalian Phenotype 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 ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology.

Usage

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

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

Smith et al. (2009) The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med, 1:390-399.

Examples

ig.MP <- dRDataLoader(RData='ig.MP')
'ig.MP' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.MP.RData?raw=true) has been loaded into the working environment (at 2017-03-27 19:59:12)
ig.MP
IGRAPH DN-- 10934 13621 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (vertex names): [1] MP:0000001->MP:0001186 MP:0000001->MP:0002006 MP:0000001->MP:0002873 [4] MP:0000001->MP:0003012 MP:0000001->MP:0003631 MP:0000001->MP:0005367 [7] MP:0000001->MP:0005369 MP:0000001->MP:0005370 MP:0000001->MP:0005371 [10] MP:0000001->MP:0005375 MP:0000001->MP:0005376 MP:0000001->MP:0005377 [13] MP:0000001->MP:0005378 MP:0000001->MP:0005379 MP:0000001->MP:0005380 [16] MP:0000001->MP:0005381 MP:0000001->MP:0005382 MP:0000001->MP:0005384 [19] MP:0000001->MP:0005385 MP:0000001->MP:0005386 MP:0000001->MP:0005387 + ... omitted several edges