dnet 1.1.2

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

Description

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

Usage

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


'org.Da.string' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/org.Da.string.RData?raw=true) has been loaded into the working environment (at 2018-01-19 12:37:48)

org.Da.string



IGRAPH 69b6ad5 UN-- 17412 751213 -- 
+ 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 69b6ad5 (vertex names):
 [1] 7680256--7695316 7678896--7695316 7674678--7675273 7674678--7676116
 [5] 7673969--7674678 7674634--7674678 7681300--7688101 7674986--7680289
 [9] 7674986--7676483 7674986--7687336 7688028--7694635 7687615--7694635
[13] 7690163--7694635 7679947--7694635 7694635--7696803 7693280--7694635
+ ... omitted several edges