Path2PPI-class {Path2PPI} | R Documentation

## Class `"Path2PPI"`

### Description

An instance of the class `Path2PPI` is the major object in the Path2PPI package. It manages all reference species and the target species. The prediction algorithm is implemented in this class as well.

### Usage

    Path2PPI(...)

### Arguments

`...` | Argument list (see Note below).

### Value

An instance of the class `Path2PPI`.

### Slots

`pathway`:

  Object of class `"character"`

`targetSpecies`:

  Object of class `".TargetSpecies"`

`referenceContainer`:

  Object of class `".ReferenceContainer"`

`h.thresh`:

  Object of class `"numeric"`

`h.range`:

  Object of class `"numeric"`

`i.thresh`:

  Object of class `"numeric"`

`consider.complexes`:

  Object of class `"logical"`

`max.complex.size`:

  Object of class `"numeric"`

`raw.ppi`:

  Object of class `"data.frame"`

`ppi`:

  Object of class `"data.frame"`

### Methods

`addReference`

  `signature(path2ppi = "Path2PPI")`

`getHybridNetwork`

  `signature(path2ppi = "Path2PPI")`

`getPPI`

  `signature(path2ppi = "Path2PPI")`

`initialize`

  `signature(.Object = "Path2PPI")`

`plot.Path2PPI`

  `signature(x = "Path2PPI")`

`predictPPI`

  `signature(path2ppi = "Path2PPI")`

`removeReference`

  `signature(path2ppi = "Path2PPI")`

`show`

  `signature(object = "Path2PPI")`

`showInteraction`

  `signature(path2ppi = "Path2PPI")`

`showReferences`

  `signature(path2ppi = "Path2PPI")`

### Note

Arguments to `Path2PPI()` and the `new` method are obligatory and must be named if they differ from this order:

pathway | A character string with the name of the pathway which has to be predicted.
targetName | A character string giving the taxonomy name of the target species.
targetId | A character string giving the taxonomy identifier of the target species.

### Author(s)

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

### Examples

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

[Package Path2PPI version 1.24.0 Index]