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