ppiNet {coexnet} | R Documentation

## Create a protein-protein interaction network

### 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 <judhenaosa@unal.edu.co>

### 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

[Package coexnet version 1.4.0 Index]