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Question: read tree fails for large trees
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gravatar for bkellman
2.6 years ago by
bkellman0
United States
bkellman0 wrote:

I'm trying to examine the DAG unifying my GO lists but there seems to be a problem converting the DOT files into trees for large numbers of GO terms (>15). I've included the code below.

Can anything be done to make readAmigoDot process up to 100 go terms? Is there another tool I can use to convert the DOT into an igraph useable format?

> tt <- readAmigoDot(getAmigoTree(goIDs=go[1:10], picType="dot", saveResult=F))
> tt <- readAmigoDot(getAmigoTree(goIDs=go[1:15], picType="dot", saveResult=F))
> tt <- readAmigoDot(getAmigoTree(goIDs=go[1:18], picType="dot", saveResult=F))
Error in `[<-`(`*tmp*`, relations[i, "parent"], relations[i, "child"],  : 
  subscript out of bounds
> tt <- readAmigoDot(getAmigoTree(goIDs=go[1:20], picType="dot", saveResult=F))
Error in `[<-`(`*tmp*`, relations[i, "parent"], relations[i, "child"],  : 
  subscript out of bounds

> dotRes <- getAmigoTree(goIDs=go[1:20], picType="dot", saveResult=F)
> tt <- readAmigoDot(object=dotRes)
Error in `[<-`(`*tmp*`, relations[i, "parent"], relations[i, "child"],  : 
  subscript out of bounds
> traceback()
1: readAmigoDot(object = dotRes)

> version
               _                           
platform       x86_64-apple-darwin13.4.0   
arch           x86_64                      
os             darwin13.4.0                
system         x86_64, darwin13.4.0        
status                                     
major          3                           
minor          2.2                         
year           2015                        
month          08                          
day            14                          
svn rev        69053                       
language       R                           
version.string R version 3.2.2 (2015-08-14)
nickname       Fire Safety   

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by bkellman0
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