ppiNet: Create a protein-protein interaction network

In gibbslab/coexnet: coexnet: An R package to build CO-EXpression NETworks from Microarray Data

Description

Creates a protein-protein interaction network using an edge list with the relations between proteins or a vector with the gene symbols or any other molecular identifier type, widely used in biological databases, to create a predictive PPI network using information of evidence in STRING database.

Usage

ppiNet(molecularIDs = NULL, file = NULL, speciesID = 9606,
  evidence = c("neighborhood", "neighborhood_transferred", "fusion",
  "cooccurence", "homology", "coexpression", "coexpression_transferred",
  "experiments", "experiments_transferred", "database", "database_transferred",
  "textmining", "textmining_transferred", "combined_score"))

Arguments

molecularIDs	A vector of IDs recognized by STRING database to create a PPI network from them.
file	A file with an edge list to charge the PPI network.
speciesID	The numerical ID from STRING database to the species of interest, by defect, is "9006" corresponding to human species.
evidence	A vector with the evidence to support the interactions between the proteins, by default is all the evidence given in STRING database.

Value

An igraph object as the protein-protein interaction network where the nodes are the molecular identifiers given in the input.

Author(s)

Juan David Henao <[e-mail]>

Examples

## Not run: 
# Creating a vector with identifiers

ID <- c("FN1","HAMP","ILK","MIF","NME1","PROCR","RAC1","RBBP7",
"TMEM176A","TUBG1","UBC","VKORC1")

# Creating the PPI network

ppi <- ppiNet(molecularIDs = ID,evidence = c("neighborhood","coexpression","experiments"))
ppi

## End(Not run)

# Creating a PPI network from external data

ppi <- ppiNet(file = system.file("extdata","ppi.txt",package = "coexnet"))
ppi

gibbslab/coexnet documentation built on May 17, 2019, 4:19 a.m.