getPPI: Get predicted PPI

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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 [email protected]

See Also

getHybridNetwork

Examples

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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)

Bioconductor-mirror/Path2PPI documentation built on May 31, 2017, 9:43 p.m.