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Last seen 10.2 years ago
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that the term is obsolete, so I don't understand why it's not working-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.
