showInteraction: Information about an interaction

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

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 [e-mail]

See Also

plot.Path2PPI,showReferences

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

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

Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
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.
Score: 1.989472
8 reference interactions: 559292 (6) 9606 (2) 
  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

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