STRINGExplore: STRINGExplore

In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

Description

STRINGExplore Utilizes the combined score and protein action information available on STRING to create an interactive network of high confidence (>0.8) interaction

Usage

STRINGExplore(systemName, STRINGactions = fetchData("STRINGactions"),
  STRINGedges = fetchData("STRINGedges0.8"),
  sysdb = fetchData("SysDB"))

Arguments

systemName	(str) A 5 character string representing the name of the desired curated gene system user would like to build a high-confidence interaction network for.
STRINGactions	(data frame) Default fetchData("STRINGactions")
STRINGedges	(data frame) Default fetchData("STRINGedges0.8")
sysdb	(list) Default fetchData("SysDB")

Value

A labeled list("nodes", "edges", "network") containing the visNetwork object and the edge and node dataframes resulting from the setup of the network. May be useful for downstream analysis by the end user.

Details

The STRING edges on their don't provide a good starting point for hypothesizing about the reasons for the existence of high- confidence interactions. By combining the easy-to-navigate, interactive network from the visNetwork package with tooltips of information from high-confidence (>0.8) data from STRING protein_actions dataset, STRINGExplore aims to ease the process of deciding on future research avenues. The graph layout takes into consideration the betweeness centrality of nodes, and so when inputting a gene list from a curated system it's highly likely that highly-centrality nodes will impart some important functionality to the system.

Author(s)

Gabriela Morgenshtern (aut)

Examples

## Not run: 
STRINGExplore("PHALY")

## End(Not run)

hyginn/BCB420.2019.ESA documentation built on May 29, 2019, 1:23 p.m.