error for the geneGOEnricher function of the NoRCE package
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Entering edit mode
Luca • 0
@lucapiacentini-9597
Last seen 1 day ago
Italy

Hello, I have already succesfully used the geneGOEnricher function of the NoRCE package in the past but now it seems there is an issue even when I use sample code as reported in the package helps, i.e.:

ncGO<-geneGOEnricher(gene = brain_disorder_ncRNA, org_assembly='hg38', near=TRUE, genetype = 'Ensembl_gene')
Error in h(simpleError(msg, call)) : 
  errore durante la valutazione dell'argomento 'object' nella selezione di un metodo per la funzione 'getTable': Unknown track: wgEncodeGencodeV31
In addition: Warning message:
In .local(x, ...) :
  'track' parameter is deprecated now you go by the 'table' instead
                Use ucscTables(genome, track) to retrieve the list of tables for a track

> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19042)

Matrix products: default


locale:
[1] LC_COLLATE=Italian_Italy.utf8  LC_CTYPE=Italian_Italy.utf8    LC_MONETARY=Italian_Italy.utf8 LC_NUMERIC=C                  
[5] LC_TIME=Italian_Italy.utf8    

time zone: Europe/Rome
tzcode source: internal

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

other attached packages:
[1] NoRCE_1.16.0

loaded via a namespace (and not attached):
  [1] later_1.3.2                 BiocIO_1.14.0               bitops_1.0-7                filelock_1.0.3             
  [5] tibble_3.2.1                XML_3.99-0.17               lifecycle_1.0.4             httr2_1.0.3                
  [9] edgeR_4.2.0                 lattice_0.22-6              alabaster.base_1.4.1        magrittr_2.0.3             
 [13] openxlsx_4.2.5.2            limma_3.60.2                yaml_2.3.8                  remotes_2.5.0              
 [17] metapod_1.12.0              httpuv_1.6.15               zip_2.3.1                   sessioninfo_1.2.2          
 [21] pkgbuild_1.4.4              DBI_1.2.3                   RColorBrewer_1.1-3          abind_1.4-5                
 [25] pkgload_1.4.0               zlibbioc_1.49.3             GenomicRanges_1.55.4        purrr_1.0.2                
 [29] BiocGenerics_0.50.0         RCurl_1.98-1.16             rappdirs_0.3.3              GenomeInfoDbData_1.2.12    
 [33] IRanges_2.37.1              S4Vectors_0.41.7            ggrepel_0.9.5               irlba_2.3.5.1              
 [37] pheatmap_1.0.12             dqrng_0.4.1                 DelayedMatrixStats_1.26.0   codetools_0.2-20           
 [41] DelayedArray_0.30.1         xml2_1.3.6                  scuttle_1.14.0              tidyselect_1.2.1           
 [45] UCSC.utils_1.0.0            ScaledMatrix_1.12.0         viridis_0.6.5               matrixStats_1.3.0          
 [49] stats4_4.4.0                BiocFileCache_2.12.0        GenomicAlignments_1.40.0    jsonlite_1.8.8             
 [53] BiocNeighbors_1.22.0        ellipsis_0.3.2              scater_1.32.1               tools_4.4.0                
 [57] progress_1.2.3              Rcpp_1.0.12                 glue_1.7.0                  gridExtra_2.3              
 [61] SparseArray_1.4.8           DESeq2_1.44.0               MatrixGenerics_1.16.0       usethis_3.0.0              
 [65] GenomeInfoDb_1.40.1         dplyr_1.1.4                 HDF5Array_1.32.0            gypsum_1.0.1               
 [69] BiocManager_1.30.25         fastmap_1.2.0               rhdf5filters_1.16.0         bluster_1.14.0             
 [73] fansi_1.0.6                 digest_0.6.35               rsvd_1.0.5                  R6_2.5.1                   
 [77] mime_0.12                   colorspace_2.1-0            GO.db_3.19.1                biomaRt_2.60.1             
 [81] RSQLite_2.3.7               celldex_1.14.0              utf8_1.2.4                  generics_0.1.3             
 [85] rtracklayer_1.64.0          prettyunits_1.2.0           httr_1.4.7                  htmlwidgets_1.6.4          
 [89] S4Arrays_1.4.1              pkgconfig_2.0.3             gtable_0.3.5                blob_1.2.4                 
 [93] SingleCellExperiment_1.26.0 XVector_0.43.1              htmltools_0.5.8.1           profvis_0.3.8              
 [97] scales_1.3.0                alabaster.matrix_1.4.0      Biobase_2.64.0              png_0.1-8                  
[101] scran_1.32.0                rstudioapi_0.16.0           reshape2_1.4.4              tzdb_0.4.0                 
[105] rjson_0.2.22                curl_5.2.1                  cachem_1.1.0                rhdf5_2.48.0               
[109] stringr_1.5.1               BiocVersion_3.19.1          parallel_4.4.0              miniUI_0.1.1.1             
[113] vipor_0.4.7                 AnnotationDbi_1.66.0        restfulr_0.0.15             pillar_1.9.0               
[117] grid_4.4.0                  alabaster.schemas_1.4.0     vctrs_0.6.5                 urlchecker_1.0.1           
[121] promises_1.3.0              BiocSingular_1.20.0         dbplyr_2.5.0                beachmat_2.20.0            
[125] xtable_1.8-4                cluster_2.1.6               beeswarm_0.4.0              readr_2.1.5                
[129] GenomicFeatures_1.56.0      cli_3.6.2                   locfit_1.5-9.9              compiler_4.4.0             
[133] Rsamtools_2.20.0            rlang_1.1.4                 crayon_1.5.3                plyr_1.8.9                 
[137] fs_1.6.4                    ggbeeswarm_0.7.2            stringi_1.8.4               viridisLite_0.4.2          
[141] alabaster.se_1.4.1          BiocParallel_1.38.0         munsell_0.5.1               Biostrings_2.72.1          
[145] devtools_2.4.5              Matrix_1.7-0                ExperimentHub_2.12.0        hms_1.1.3                  
[149] sparseMatrixStats_1.16.0    bit64_4.0.5                 ggplot2_3.5.1               Rhdf5lib_1.26.0            
[153] KEGGREST_1.44.1             statmod_1.5.0               shiny_1.9.1                 SummarizedExperiment_1.34.0
[157] alabaster.ranges_1.4.2      AnnotationHub_3.12.0        igraph_2.0.3                memoise_2.0.1              
[161] bit_4.0.5

Could you provide some help to fix this error?

Thanks in advance!

NoRCE • 231 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 18 hours ago
United States

This will likely require the maintainer of that package to fix. Note the error you get (or at least the English version of):

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'getTable': Unknown track: wgEncodeGencodeV31lift37

If you go to the UCSC Genome browser, choose hg19, and then open the table browser, then click the down arrow in the Table drop-down, and then go down to the wgEncodeGencode section, you will not find wgEncodeGencodeV31lift37. Which is what the error is telling you - that table no longer exists.

I don't know if there are other tables that contain essentially the same information that could be used by NoRCE, but the maintainer might, so you might contact the maintainer directly.

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