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Last data update: 2014.03.03

R: Information about an interaction

showInteraction

R Documentation

Information about an interaction

Description

Use showInteraction to get detailed information about one interaction of the predicted PPI.

Usage

showInteraction(path2ppi, interaction, mode="default", verbose=TRUE)

Arguments

`path2ppi`	An object from the class `Path2PPI`.
`interaction`	Character vector consisting of the identifiers of the two interactors.
`mode`	Character string. Which information of this interaction is requested. "default": only the predicted interaction and some major information are provided. "detailed": all interactions deduced from each reference species with this interaction is provided. "references": each reference interaction of the current interaction with some major information. "references.detailed": each reference interaction of the current interaction with all available information (extracted from the corresponding iRefIndex data set).
`verbose`	Logical. `FALSE` hides messages in the output.

Value

Data frame with the requested information defined in mode.

Author(s)

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

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,h.range=c(1e-60,1e-20))

interaction <- showInteraction(ppi,interaction=c("B2AT71","B2AE79"),
mode="detailed")
interaction

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.
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Type 'license()' or 'licence()' for distribution details.

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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
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> 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/showInteraction.Rd_%03d_medium.png", width=480, height=480)
> ### Name: showInteraction
> ### Title: Information about an interaction
> ### Aliases: showInteraction showInteraction-methods
> 
> ### ** 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)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
> ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", 
+                     yeast.ai.proteins, yeast.ai.irefindex, 
+                     pa2yeast.ai.homologs)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
>                     
> ppi <- predictPPI(ppi,h.range=c(1e-60,1e-20))
Begin with Homo sapiens
6 interactions processed. These lead to 5 interactions in target species.
-------------------------------
Begin with Saccharomyces cerevisiae (S288c)
15 interactions processed. These lead to 22 interactions in target species.
-------------------------------
Combine results to one single PPI.
A total of 13 putative interactions were predicted in target species.
> 
> interaction <- showInteraction(ppi,interaction=c("B2AT71","B2AE79"),
+ mode="detailed")
Score: 1.989472
8 reference interactions: 559292 (6) 9606 (2) 
> interaction
  source.id target.id score h.scoreA h.scoreB r.species r.species.s r.species.t
1    B2AT71    B2AE79 0.855     0.71     1.00      9606      P42345      P42345
2    B2AT71    B2AE79 0.820     0.64     1.00    559292      P35169      P32600
3    B2AT71    B2AE79 0.825     0.65     1.00    559292      P32600      P32600
4    B2AT71    B2AE79 0.820     0.64     1.00    559292      P35169      P35169
5    B2AE79    B2AT71 0.855     1.00     0.71      9606      P42345      P42345
6    B2AE79    B2AT71 0.825     1.00     0.65    559292      P35169      P32600
7    B2AE79    B2AT71 0.825     1.00     0.65    559292      P32600      P32600
8    B2AE79    B2AT71 0.820     1.00     0.64    559292      P35169      P35169
  pos.edges used.edges    ref
1         6          4 742389
2         6          4 522660
3         6          4 858136
4         6          4 105672
5         6          4 742389
6         6          4 522660
7         6          4 858136
8         6          4 105672
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>