dnet 1.1.2

C.elegans functional protein association network from STRING (version 10).

Description

An igraph object that contains a functional protein association network in c.elegans. The network is extracted from the STRING database (version 10). Only those associations with medium confidence (score>=0.4) are retained.

Usage

org.Ce.string <- dRDataLoader(RData = "org.Ce.string")

Value

an object of class "igraph" (see http://igraph.org/r/doc/aaa-igraph-package.html). It has attributes for both vertices and edges. Below are attributes for the vertices:

  • name: unique id for the vertices
  • seqid: protein seqid for the vertices
  • geneid: Entrez geneid (if any) for the vertices
  • symbol: gene symbol (if any) for the vertices
  • description: gene description (if any) for the vertices

Below are attributes for the edges:

  • neighborhood_score: predictive score based on neighborhood data
  • fusion_score: predictive score based on fusion data
  • cooccurence_score: predictive score based on cooccurence data
  • coexpression_score: predictive score based on coexpression
  • experimental_score: predictive score based on experimental data
  • database_score: predictive score based on database
  • textmining_score: predictive score based on text mining
  • combined_score: combined score from all above predictive scores

References

Szklarczyk et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res, 43:D447-52.

Examples

org.Ce.string <- dRDataLoader(RData='org.Ce.string')


'org.Ce.string' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/org.Ce.string.RData?raw=true) has been loaded into the working environment (at 2018-01-19 12:37:37)

org.Ce.string



IGRAPH 7199b2e UN-- 13832 626600 -- 
+ attr: name (v/c), seqid (v/c), geneid (v/n), symbol (v/c),
| description (v/c), neighborhood_score (e/n), fusion_score (e/n),
| cooccurence_score (e/n), coexpression_score (e/n), experimental_score
| (e/n), database_score (e/n), textmining_score (e/n), combined_score
| (e/n)
+ edges from 7199b2e (vertex names):
 [1] 2892761--2906027 2895221--2895814 2895814--2904557 2895814--2901851
 [5] 2895814--2906736 2909201--2911889 2898279--2911889 2899725--2911889
 [9] 2898803--2911889 2906003--2908369 2899221--2906003 2901210--2906003
[13] 2905292--2906003 2894603--2900567 2900567--2905292 2900567--2908735
+ ... omitted several edges