PANTHER.db function not found
1
0
Entering edit mode
krc3004 ▴ 10
@krc3004-12978
Last seen 6.5 years ago

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     

pantherdb goseq biomart • 1.5k views
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1
Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 55 minutes ago
EMBL Heidelberg

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.

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