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Question: custom annotation for GO enrichment
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gravatar for cabezasdelafuented
3 months ago by
cabezasdelafuented10 wrote:

I'm trying to create a custom annotation for Human genes using the package annotationForge and then run an enrichment analysis using the package clusterProfiler. I am able to construct the necessary data frames for the function makeOrgPackage() retrieving the information from the Homo.sapiens package of the GO I'm interested in using. My problem comes when I try to run the function makeOrgPackage() which returns the following error:

Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating go table:
Error in rsqlite_send_query(conn@ptr, statement) : 
  NOT NULL constraint failed: go.GO
In addition: There were 15 warnings (use warnings() to see them)
 

I have also noticed that some of the gene ontologies that I'm trying to retrieve from the Homo.sapiens package don't appear (like GO:0099536).

Thank you all.

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.6

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

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

other attached packages:
 [1] org.Hsapiens2.eg.db_0.1                
 [2] AnnotationForge_1.16.1                 
 [3] RamiGO_1.20.0                          
 [4] gsubfn_0.6-6                           
 [5] proto_1.0.0                            
 [6] BiocInstaller_1.24.0                   
 [7] Homo.sapiens_1.3.1                     
 [8] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [9] GO.db_3.4.0                            
[10] OrganismDbi_1.16.0                     
[11] GenomicFeatures_1.26.4                 
[12] GOSemSim_2.0.4                         
[13] GOplot_1.0.2                           
[14] gridExtra_2.2.1                        
[15] ggrepel_0.6.5                          
[16] sva_3.22.0                             
[17] genefilter_1.56.0                      
[18] mgcv_1.8-18                            
[19] nlme_3.1-131                           
[20] reshape2_1.4.2                         
[21] ggdendro_0.1-20                        
[22] gplots_3.0.1                           
[23] RColorBrewer_1.1-2                     
[24] ggpubr_0.1.4                           
[25] magrittr_1.5                           
[26] ReactomePA_1.18.1                      
[27] pathview_1.14.0                        
[28] org.Hs.eg.db_3.4.0                     
[29] AnnotationDbi_1.36.2                   
[30] clusterProfiler_3.2.14                 
[31] DOSE_3.0.10                            
[32] biomaRt_2.30.0                         
[33] oce_0.9-21                             
[34] gsw_1.0-4                              
[35] testthat_1.0.2                         
[36] regionReport_1.8.2                     
[37] pheatmap_1.0.8                         
[38] ggplot2_2.2.1                          
[39] ape_4.1                                
[40] DESeq2_1.14.1                          
[41] SummarizedExperiment_1.4.0             
[42] Biobase_2.34.0                         
[43] GenomicRanges_1.26.4                   
[44] GenomeInfoDb_1.10.3                    
[45] IRanges_2.8.2                          
[46] S4Vectors_0.12.2                       
[47] BiocGenerics_0.20.0                    

loaded via a namespace (and not attached):
  [1] RSQLite_2.0              htmlwidgets_0.9         
  [3] grid_3.3.3               BiocParallel_1.8.2      
  [5] munsell_0.4.3            codetools_0.2-15        
  [7] colorspace_1.3-2         knitr_1.16              
  [9] KEGGgraph_1.32.0         bit64_0.9-7             
 [11] rprojroot_1.2            R6_2.2.2                
 [13] markdown_0.8             locfit_1.5-9.1          
 [15] bitops_1.0-6             fgsea_1.0.2             
 [17] assertthat_0.2.0         scales_0.4.1            
 [19] nnet_7.3-12              derfinder_1.8.5         
 [21] gtable_0.2.0             rlang_0.1.1             
 [23] splines_3.3.3            rtracklayer_1.34.2      
 [25] lazyeval_0.2.0           acepack_1.4.1           
 [27] checkmate_1.8.3          backports_1.1.0         
 [29] qvalue_2.6.0             Hmisc_4.0-3             
 [31] RBGL_1.50.0              tools_3.3.3             
 [33] tcltk_3.3.3              RCytoscape_1.24.1       
 [35] Rcpp_0.12.12             plyr_1.8.4              
 [37] base64enc_0.1-3          zlibbioc_1.20.0         
 [39] RCurl_1.95-4.8           rpart_4.1-11            
 [41] bumphunter_1.14.0        GenomicFiles_1.10.3     
 [43] cluster_2.0.6            data.table_1.10.4       
 [45] DO.db_2.9                reactome.db_1.58.0      
 [47] matrixStats_0.52.2       evaluate_0.10.1         
 [49] xtable_1.8-2             XML_3.98-1.9            
 [51] tibble_1.3.3             KernSmooth_2.23-15      
 [53] crayon_1.3.2             htmltools_0.3.6         
 [55] Formula_1.2-2            tidyr_0.6.3             
 [57] geneplotter_1.52.0       lubridate_1.6.0         
 [59] DBI_0.7                  MASS_7.3-47             
 [61] rappdirs_0.3.1           XMLRPC_0.3-0            
 [63] Matrix_1.2-10            gdata_2.18.0            
 [65] derfinderHelper_1.8.1    bindr_0.1               
 [67] igraph_1.1.2             pkgconfig_2.0.1         
 [69] GenomicAlignments_1.10.1 registry_0.3            
 [71] RefManageR_0.14.12       foreign_0.8-69          
 [73] xml2_1.1.1               foreach_1.4.3           
 [75] annotate_1.52.1          rngtools_1.2.4          
 [77] DEFormats_1.2.0          pkgmaker_0.22           
 [79] XVector_0.14.1           bibtex_0.4.2            
 [81] knitcitations_1.0.8      doRNG_1.6.6             
 [83] stringr_1.2.0            VariantAnnotation_1.20.3
 [85] digest_0.6.12            graph_1.52.0            
 [87] Biostrings_2.42.1        rmarkdown_1.6           
 [89] fastmatch_1.1-0          htmlTable_1.9           
 [91] edgeR_3.16.5             Rsamtools_1.26.2        
 [93] gtools_3.5.0             graphite_1.20.1         
 [95] knitrBootstrap_1.0.1     jsonlite_1.5            
 [97] bindrcpp_0.2             limma_3.30.13           
 [99] BSgenome_1.42.0          lattice_0.20-35         
[101] KEGGREST_1.14.1          httr_1.2.1              
[103] survival_2.41-3          glue_1.1.1              
[105] png_0.1-7                iterators_1.0.8         
[107] bit_1.1-12               Rgraphviz_2.18.0        
[109] stringi_1.1.5            blob_1.1.0              
[111] latticeExtra_0.6-28      caTools_1.17.1          
[113] memoise_1.1.0            dplyr_0.7.2 

2

It seems you are trying to do some fancy stuff, but it's not clear why. Is there some reason that the existing annotation packages are not useful to you?

ADD REPLYlink written 3 months ago by James W. MacDonald45k

I want to remove certain genes from the annotation to see if the signal I have is due to specific genes or it's all the group that is involved

ADD REPLYlink written 3 months ago by cabezasdelafuented10

Rather than trying to rebuild a new package, why don't you use the data.frame format that is described in the clusterProfiler vignette? It would be simple to do what you want that way.

ADD REPLYlink written 3 months ago by James W. MacDonald45k
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