Path2PPI: Class '"Path2PPI"'

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

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 [e-mail]

Examples

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

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

Autophagy induction in Podospora anserina (5145)
------------------------------------------------- 
No reference species yet.
------------------------------------------------- 
No predicted PPI yet.

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