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Question: PANTHER.db function not found
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gravatar for krc3004
3 months ago by
krc300410
krc300410 wrote:

Hi all,

I'm using PANTHER.db to run some enrichment analysis and am trying to use the function pthOrganisms to restrict the database to mouse.  More specifically, the code is:

pthOrganisms(PANTHER.db) = "MOUSE"

However, I obtained the following error:

Error: could not find function "pthOrganisms"

The package installs just fine and the library loads correctly.  Page 3 of the vignette (https://bioconductor.org/packages/release/data/annotation/vignettes/PANTHER.db/inst/doc/PANTHER.db.pdf) shows how to use the command, and my code matches exactly.  I also tried PANTHER.db::pthOrganisms(PANTHER.db) = "MOUSE" but still obtained the same error.  Any tips on how to proceed?

Thanks very much!

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Mm.eg.db_3.0.0                     biomaRt_2.22.0                         TxDb.Mmusculus.UCSC.mm10.ensGene_3.0.0
 [4] GenomicFeatures_1.18.7                 reactome.db_1.48.0                     PANTHER.db_1.0.1                      
 [7] KEGGREST_1.6.4                         goseq_1.18.0                           AnnotationDbi_1.28.2                  
[10] Biobase_2.26.0                         RSQLite_1.0.0                          DBI_0.3.1                             
[13] geneLenDataBase_1.1.1                  BiasedUrn_1.06.1                       XVector_0.6.0                         
[16] BiocInstaller_1.16.5                   pheatmap_1.0.2                         ggplot2_1.0.1                         
[19] data.table_1.9.4                       dplyr_0.4.1                            plyr_1.8.2                            
[22] tidyr_0.2.0                            Rsubread_1.16.1                        DESeq2_1.6.3                          
[25] RcppArmadillo_0.5.100.1.0              Rcpp_0.11.6                            rtracklayer_1.26.3                    
[28] GenomicRanges_1.18.4                   GenomeInfoDb_1.2.5                     IRanges_2.0.1                         
[31] S4Vectors_0.4.0                        BiocGenerics_0.12.1                   

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3         annotate_1.44.0         assertthat_0.1          base64enc_0.1-2         BatchJobs_1.6           BBmisc_1.9             
 [7] BiocParallel_1.0.3      Biostrings_2.34.1       bitops_1.0-6            brew_1.0-6              checkmate_1.5.3         chron_2.3-45           
[13] cluster_2.0.1           codetools_0.2-11        colorspace_1.2-6        digest_0.6.8            fail_1.2                foreach_1.4.2          
[19] foreign_0.8-63          Formula_1.2-1           genefilter_1.48.1       geneplotter_1.44.0      GenomicAlignments_1.2.2 GO.db_3.0.0            
[25] grid_3.1.2              gridExtra_0.9.1         gtable_0.1.2            Hmisc_3.16-0            httr_0.6.1              iterators_1.0.7        
[31] labeling_0.3            lattice_0.20-31         latticeExtra_0.6-26     locfit_1.5-9.1          magrittr_1.5            MASS_7.3-40            
[37] Matrix_1.2-0            mgcv_1.8-6              munsell_0.4.2           nlme_3.1-120            nnet_7.3-9              png_0.1-7              
[43] proto_0.3-10            RColorBrewer_1.1-2      RCurl_1.95-4.6          reshape2_1.4.1          rpart_4.1-9             Rsamtools_1.18.3       
[49] scales_0.2.4            sendmailR_1.2-1         splines_3.1.2           stringi_0.4-1           stringr_1.0.0           survival_2.38-1        
[55] tools_3.1.2             XML_3.98-1.1            xtable_1.7-4            zlibbioc_1.12.0     

ADD COMMENTlink modified 3 months ago by Mike Smith2.1k • written 3 months ago by krc300410
1
gravatar for Mike Smith
3 months ago by
Mike Smith2.1k
EMBL Heidelberg / de.NBI
Mike Smith2.1k wrote:

You're using a very old version of R, 3.1.2 is now nearly 3 years old.  Since Bioconductor releases (and thus versions of Bioconductor packages) are tied to the R version that you are using, this means you also get very old versions of the packages.  In your sessionInfo() output you can see that you have PANTHER.db_1.0.1, but the most recent version is PANTHER.db_1.0.3

If you check the old vignette for version 1.0.1 (https://bioconductor.org/packages/3.1/data/annotation/vignettes/PANTHER.db/inst/doc/PANTHER.db.pdf) you'll see that function doesn't appear as it is a relatively new addition.

My recommendation would be to get the latest version of R and freshly install the packages you want to use.

ADD COMMENTlink written 3 months ago by Mike Smith2.1k
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