[BioC] ontoCompare

[Agnes Paquet]

Hi Brad,

I will take a look and see if there is an easy fix. Sorry for the trouble you are having using the package.

Agnes

On Jul 12, 2012, at 12:29 PM, Brad Davis [guest] <guest at bioconductor.org> wrote:

> 
> Hello everyone,
> 
> I am having some difficulty with ontoCompare when providing it with a list of GO terms.  Here is an example of the output that I get when the function fails:
> 
> 
>> ontoTest <- ontoCompare(list(gotermslist), probeType="GO", goType="BP", plot=TRUE)
> Starting ontoCompare...
> Error in goidvect[test] : invalid subscript type 'list'
> 
> Enter a frame number, or 0 to exit   
> 
> 1: ontoCompare(list(gotermslist), probeType = "GO", goType = "BP", plot = TRUE)
> 2: lapply(tmp, parentsVectWraper, endnode)
> 3: FUN(X[[2554]], ...)
> 
>> gotermslist[2554] 
> [1] "GO:0051605"
> 
> Using Amigo to look up this GO term shows this GO ID is an alternate ID to GO:0016485, but using the Synonym function from GO.db on GO:0051605 doesn't provide any useful information.
> 
> 
>> Synonym("GO:0051605")
> $<NA>
> NULL
> 
> Conversely, running Synonym on GO:0016485 identifies GO:0051605 as a valid alternate id
> 
> 
>> Synonym("GO:0016485")
> $`GO:0016485`
> [1] "peptidolysis during protein maturation"       
> [2] "protein maturation by peptide bond cleavage"  
> [3] "protein maturation by peptide bond hydrolysis"
> [4] "protein maturation by proteolysis"            
> [5] "GO:0051605"                                   
> 
> I run into the same problem with GO:0006345, which is an alternate ID for GO:0031936 (which doesn't cause a problem for ontoCompare).
> 
> It seems like this represents some sort of mapping problem with GO.db, but I don't know how to address it myself.  Any suggestions?
> 
> In other cases, ontoCompare fails when there doesn't seem to be any problem with the GO id, at least so far as I can tell, e.g. GO:0055086. Amigo doesn't show any alternate ids nor does it indicate that the term is obsolete, so I don't understand why it's not working- but it is very frustrating.
> 
> I would appreciate any suggestions.
> 
> 
> 
> 
> 
> 
> -- output of sessionInfo(): 
> 
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
> 
> locale:
> [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252   
> [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
> [5] LC_TIME=English_Canada.1252    
> 
> attached base packages:
> [1] compiler  grid      stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] Vennerable_2.2        xtable_1.7-0          reshape_0.8.4         plyr_1.7.1           
> [5] RColorBrewer_1.0-5    lattice_0.20-6        RBGL_1.30.1           graph_1.32.0         
> [9] manipulate_0.96.316   annotate_1.32.3       goTools_1.28.0        GO.db_2.6.1          
> [13] RSQLite_0.11.1        DBI_0.2-5             AnnotationDbi_1.16.19 Biobase_2.14.0       
> [17] nlme_3.1-104          car_2.0-12            nnet_7.3-4            gplots_2.11.0        
> [21] MASS_7.3-19           KernSmooth_2.23-8     caTools_1.13          bitops_1.0-4.1       
> [25] gdata_2.11.0          gtools_2.7.0         
> 
> loaded via a namespace (and not attached):
> [1] IRanges_1.12.6 tools_2.15.1  
> 
> --
> Sent via the guest posting facility at bioconductor.org.