getPPI: Get predicted PPI

In Path2PPI: Prediction of pathway-related protein-protein interaction networks

Description

Get the predicted PPI of an Path2PPI object consisting of each predicted interaction and protein in the target species.

Usage

getPPI(path2ppi, raw=FALSE, igraph=FALSE)

Arguments

path2ppi	An object of the class Path2PPI.
raw	Logical; if TRUE then the detailed view of the predicted PPI will be returned. That means that each predicted interaction deduced from each reference species is given. In contrast, FALSE leads to the actually predicted and combined PPI where no redundancies occur.
igraph	Logical; if TRUE then the returned PPI is given as igraph-object. Otherwise a data frame with each predicted interaction will be returned.

Value

See igraph argument.

Author(s)

Oliver Philipp [e-mail]

See Also

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)
ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", 
                    yeast.ai.proteins, yeast.ai.irefindex, 
                    pa2yeast.ai.homologs)

ppi <- predictPPI(ppi)

#Get the predicted PPI as data frame.
network <- getPPI(ppi)

#Get the detailed predicted PPI as data frame.
network.raw <- getPPI(ppi,raw=TRUE)

Example output

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

Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
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.

Path2PPI documentation built on Nov. 8, 2020, 5:38 p.m.