getPPI {Path2PPI} | R Documentation

## Get predicted PPI

### 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 MolBI-software@bioinformatik.uni-frankfurt.de

### 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)

[Package Path2PPI version 1.12.0 Index]