goseq package: cannot find function supportedOrganisms()

Question

[mrodrigues.fernanda]

Hi!

I am trying to use the package goseq, but when I try running the function supportedOrganisms() R says it cannot find it. Does anyone know what might be the reason?

Thanks!

sessionInfo()

R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] KEGG.db_3.2.2         goseq_1.22.0         
 [3] geneLenDataBase_1.6.0 BiasedUrn_1.07       
 [5] GOstats_2.36.0        graph_1.48.0         
 [7] Category_2.36.0       GO.db_3.2.2          
 [9] Matrix_1.2-4          org.Bt.eg.db_3.2.3   
[11] AnnotationDbi_1.32.3  edgeR_3.12.0         
[13] limma_3.26.9          affycoretools_1.42.0 
[15] Biobase_2.30.0        WGCNA_1.51           
[17] RSQLite_1.0.0         DBI_0.3.1            
[19] fastcluster_1.1.16    dynamicTreeCut_1.63-1
[21] rtracklayer_1.30.4    GenomicRanges_1.22.4 
[23] GenomeInfoDb_1.6.3    IRanges_2.4.8        
[25] S4Vectors_0.8.11      BiocGenerics_0.16.1  

loaded via a namespace (and not attached):
 [1] nlme_3.1-126               bitops_1.0-6              
 [3] matrixStats_0.50.1         doParallel_1.0.10         
 [5] RColorBrewer_1.1-2         gcrma_2.42.0              
 [7] tools_3.2.4                affyio_1.40.0             
 [9] KernSmooth_2.23-15         rpart_4.1-10              
[11] mgcv_1.8-12                Hmisc_3.17-2              
[13] colorspace_1.2-6           nnet_7.3-12               
[15] gridExtra_2.2.1            GGally_1.0.1              
[17] DESeq2_1.10.1              bit_1.1-12                
[19] preprocessCore_1.32.0      ggbio_1.18.5              
[21] caTools_1.17.1             scales_0.4.0              
[23] genefilter_1.52.1          affy_1.48.0               
[25] RBGL_1.46.0                stringr_1.0.0             
[27] Rsamtools_1.22.0           foreign_0.8-66            
[29] R.utils_2.2.0              AnnotationForge_1.12.2    
[31] XVector_0.10.0             dichromat_2.0-0           
[33] BSgenome_1.38.0            PFAM.db_3.2.2             
[35] impute_1.44.0              BiocInstaller_1.20.1      
[37] hwriter_1.3.2              gtools_3.5.0              
[39] BiocParallel_1.4.3         acepack_1.3-3.3           
[41] R.oo_1.20.0                VariantAnnotation_1.16.4  
[43] RCurl_1.95-4.8             magrittr_1.5              
[45] Formula_1.2-1              oligoClasses_1.32.0       
[47] futile.logger_1.4.1        Rcpp_0.12.4               
[49] munsell_0.4.3              R.methodsS3_1.7.1         
[51] stringi_1.0-1              SummarizedExperiment_1.0.2
[53] zlibbioc_1.16.0            gplots_3.0.1              
[55] plyr_1.8.3                 grid_3.2.4                
[57] gdata_2.17.0               ReportingTools_2.10.0     
[59] lattice_0.20-33            Biostrings_2.38.4         
[61] splines_3.2.4              GenomicFeatures_1.22.13   
[63] annotate_1.48.0            locfit_1.5-9.1            
[65] knitr_1.12.3               geneplotter_1.48.0        
[67] reshape2_1.4.1             codetools_0.2-14          
[69] biomaRt_2.26.1             futile.options_1.0.0      
[71] XML_3.98-1.4               RcppArmadillo_0.6.600.4.0 
[73] biovizBase_1.18.0          latticeExtra_0.6-28       
[75] lambda.r_1.1.7             foreach_1.4.3             
[77] gtable_0.2.0               reshape_0.8.5             
[79] ggplot2_2.1.0              xtable_1.8-2              
[81] ff_2.2-13                  survival_2.38-3           
[83] OrganismDbi_1.12.1         iterators_1.0.8           
[85] GenomicAlignments_1.6.3    cluster_2.0.3             
[87] GSEABase_1.32.0

[James Ashmore]

I can't find a reference to a function named supportedOrganisms in the goseq package, maybe you mean supportedGenomes?

[mrodrigues.fernanda]

I found it here: https://bioconductor.org/packages/3.3/bioc/vignettes/goseq/inst/doc/goseq.pdf

Maybe it has been replaced by supportedGenomes() ?

Answer 1

[James Ashmore]

It looks to be the case, I had a look in the geneLenDataBase package which you also need and they only have a reference to a function called supportedGenomes. Try that instead.

EDIT:

The developmental version of goseq has the function supportedOrganisms. Install the developmental version.

[mrodrigues.fernanda]

You're right. I installed the development version and the function is there. Thank you so much, James! You were very helpful.