Information about reference species

Description

Get information about the currently stored reference species. If indicated by returnValue a data frame - containing information about each protein or interaction - is provided as well.

Usage

showReferences(path2ppi, species = NA, returnValue = NA)

Arguments

Value

See description for returnValue

Author(s)

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

See Also

addReference, removeReference, showInteraction

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) 

#Get general information about each stored reference species
showReferences(ppi)

#Get general information about reference species with the taxonomy id "9606"
showReferences(ppi, species="9606")

#Get all proteins associated with the pathway of interest 
#and previously given by the user
proteins <- showReferences(ppi, species="9606", returnValue="proteins")

#Get all processed and non-redundant interactions previously 
#determined to be relevant for the pathway of interest
interactions <- showReferences(ppi, species="9606", returnValue="interactions")

#Get all relevant interactions in the detailed irefindex format
irefindex <- showReferences(ppi, species="9606", returnValue="irefindex")

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/showReferences.Rd_%03d_medium.png", width=480, height=480)
> ### Name: showReferences
> ### Title: Information about reference species
> ### Aliases: 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)
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.
> 
> #Get general information about each stored reference species
> showReferences(ppi)
Homo sapiens (TaxId: 9606)
--------------------------- 
5 proteins (0 not used)
894 interactions:
- 6 interactions have both interactors in protein list.
- 349 interactions have at least one interactor in protein list.
- 660 interactions in 102 protein complexes.


Saccharomyces cerevisiae (S288c) (TaxId: 559292)
------------------------------------------------- 
7 proteins (0 not used)
2910 interactions:
- 15 interactions have both interactors in protein list.
- 834 interactions have at least one interactor in protein list.
- 2207 interactions in 102 protein complexes.


> 
> #Get general information about reference species with the taxonomy id "9606"
> showReferences(ppi, species="9606")
Homo sapiens (TaxId: 9606)
--------------------------- 
5 proteins (0 not used)
894 interactions:
- 6 interactions have both interactors in protein list.
- 349 interactions have at least one interactor in protein list.
- 660 interactions in 102 protein complexes.
> 
> #Get all proteins associated with the pathway of interest 
> #and previously given by the user
> proteins <- showReferences(ppi, species="9606", returnValue="proteins")
> 
> #Get all processed and non-redundant interactions previously 
> #determined to be relevant for the pathway of interest
> interactions <- showReferences(ppi, species="9606", returnValue="interactions")
> 
> #Get all relevant interactions in the detailed irefindex format
> irefindex <- showReferences(ppi, species="9606", returnValue="irefindex")
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>