dnet 1.1.2

Fruitfly functional protein association network from STRING (version 10).

Description

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

Usage

org.Dm.string <- dRDataLoader(RData = "org.Dm.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.Dm.string <- dRDataLoader(RData='org.Dm.string')


'org.Dm.string' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/org.Dm.string.RData?raw=true) has been loaded into the working environment (at 2018-01-19 12:38:00)

org.Dm.string



IGRAPH 1ea5a88 UN-- 12189 452804 -- 
+ 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 1ea5a88 (vertex names):
 [1] 2544078--2546855 2535389--2544078 2542494--2544078 2540465--2544322
 [5] 2541136--2543785 2537825--2539474 2538375--2539474 2537360--2547122
 [9] 2540628--2541382 2536177--2536641 2542127--2543894 2540304--2541268
[13] 2536652--2540445 2545864--2548656 2547309--2548195 2536395--2547817
+ ... omitted several edges