R: Get hybrid network of the predicted PPI

getHybridNetwork {Path2PPI}

R Documentation

Get hybrid network of the predicted PPI

Description

Get the hybrid network of the previously predicted PPI. The hybrid network consists of all relevant interactions from the reference species, the predicted interactions in the target species and all relevant homologous relationships.

Usage

getHybridNetwork(path2ppi, igraph = FALSE)

Arguments

`path2ppi`	An object of the class `Path2PPI`.
`igraph`	Logical; if `TRUE` then the hybrid network is given as igraph-object. Otherwise a data frame, consisting of each interaction and homologous relationship, will be returned.

Value

See igraph argument.

Author(s)

Oliver Philipp MolBI-software@bioinformatik.uni-frankfurt.de

Examples

data(ai) #Load test data set

ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")

ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins, 
                    human.ai.irefindex, pa2human.ai.homologs)
ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", 
                    yeast.ai.proteins, yeast.ai.irefindex, 
                    pa2yeast.ai.homologs)

ppi <- predictPPI(ppi)

#Return the hybrid network as data frame
hybrid <- getHybridNetwork(ppi)

#Return the hybrid network as igraph object
hybrid <- getHybridNetwork(ppi,igraph=TRUE)

[Package Path2PPI version 1.10.0 Index]