[BioC] ontoCompare

[Brad Davis [guest]]

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 Amigo doesn't show any alternate ids nor does it indicate that the term is obsolete, so I don't understand why it's not working- but it is very frustrating.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  

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