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

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:

Author(s)

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

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Path2PPI)
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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Path2PPI/Path2PPI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Path2PPI-class
> ### Title: Class '"Path2PPI"'
> ### Aliases: Path2PPI-class Path2PPI addReference,Path2PPI-method
> ###   getHybridNetwork,Path2PPI-method getPPI,Path2PPI-method
> ###   initialize,Path2PPI-method plot.Path2PPI,Path2PPI-method
> ###   predictPPI,Path2PPI-method removeReference,Path2PPI-method
> ###   show,Path2PPI-method showInteraction,Path2PPI-method
> ###   showReferences,Path2PPI-method
> 
> ### ** Examples
> 
> ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")
> ppi
Autophagy induction in Podospora anserina (5145)
------------------------------------------------- 
No reference species yet.
------------------------------------------------- 
No predicted PPI yet.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>