Dear all,
I'm using GOSemSim for computing semantic similarities between GO terms.
When I performed the similarity analysis with Wang method there are no problem:
> library("GOSemSim")
> hsGOBP <- godata('org.Hs.eg.db', ont="BP")
preparing gene to GO mapping data...
preparing IC data...
> goSim("GO:0042346", "GO:0042346", semData=hsGOBP, measure="Wang")
[1] 1
But if I change the method to Resnik, Rel, Jiang or Lin, the analysis generate only one NA as result:
> goSim("GO:0042346", "GO:0042346", semData=hsGOBP, measure="Rel")
[1] NA
Manipulating the vector I discovered that the error is produced by secondary GO term, GO:0042346 (above).
Are there an alternative to analyze a vector with secondary GO terms?
Thanks Luis Arge
--
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale:
[1] LC_CTYPE=pt_BR.UTF-8 LC_NUMERIC=C LC_TIME=pt_BR.UTF-8
[4] LC_COLLATE=pt_BR.UTF-8 LC_MONETARY=pt_BR.UTF-8 LC_MESSAGES=pt_BR.UTF-8
[7] LC_PAPER=pt_BR.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Hs.eg.db_3.7.0 AnnotationDbi_1.44.0 IRanges_2.16.0 S4Vectors_0.20.1
[5] Biobase_2.42.0 BiocGenerics_0.28.0 GOSemSim_2.8.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 GO.db_3.7.0 digest_0.6.18 DBI_1.0.0 RSQLite_2.1.1
[6] blob_1.1.1 tools_3.5.1 bit64_0.9-7 bit_1.1-14 compiler_3.5.1
[11] pkgconfig_2.0.2 memoise_1.1.0
Thank you Guangchuang.
I'll verify all GO terms and then replace by their primary GO.
--
Luis Arge