Remove reference species

Description

Remove reference species previously attached to an object from the class Path2PPI.

Usage

removeReference(path2ppi, species)

Arguments

Value

An object of the class Path2PPI with removed reference species species.

Author(s)

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

See Also

showReferences, addReference

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) 

#Remove second reference species
ppi <- removeReference(ppi,2)

#Remove reference species with taxonomy id "9606"
ppi <- removeReference(ppi,"9606") 

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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'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/removeReference.Rd_%03d_medium.png", width=480, height=480)
> ### Name: removeReference
> ### Title: Remove reference species
> ### Aliases: removeReference
> 
> ### ** 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.
> 
> #Remove second reference species
> ppi <- removeReference(ppi,2)
> 
> #Remove reference species with taxonomy id "9606"
> ppi <- removeReference(ppi,"9606") 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>