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

Value

See igraph argument.

Author(s)

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

See Also

getPPI

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Path2PPI)
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Path2PPI/getHybridNetwork.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getHybridNetwork
> ### Title: Get hybrid network of the predicted PPI
> ### Aliases: getHybridNetwork
> 
> ### ** 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)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
> ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", 
+                     yeast.ai.proteins, yeast.ai.irefindex, 
+                     pa2yeast.ai.homologs)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
> 
> ppi <- predictPPI(ppi)
Begin with Homo sapiens
6 interactions processed. These lead to 0 interactions in target species.
-------------------------------
Begin with Saccharomyces cerevisiae (S288c)
15 interactions processed. These lead to 8 interactions in target species.
-------------------------------
Combine results to one single PPI.
A total of 8 putative interactions were predicted in target species.
> 
> #Return the hybrid network as data frame
> hybrid <- getHybridNetwork(ppi)
> 
> #Return the hybrid network as igraph object
> hybrid <- getHybridNetwork(ppi,igraph=TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>