Error in mapping the gene names to the STRINGdb identifiers
Entering edit mode
Last seen 7 weeks ago
Iowa State University

I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but giving an error for version 11.5. Also, the StringDB version 11 is not accessible by the package.

string_db <- STRINGdb$new(version="11.5", species=9606,score_threshold=700, input_directory="")
geneMapped <- string_db$map(data.frame(gene=geneList), "gene", removeUnmappedRows = TRUE)

Error in `[.data.frame`(x, r, vars, drop = drop) : 
  undefined columns selected

sessionInfo( )

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

[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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] WGCNA_1.70-3           fastcluster_1.2.3      dynamicTreeCut_1.63-1  RSQLite_2.2.7          rDGIdb_1.16.0          openxlsx_4.2.4        
 [7]    AnnotationDbi_1.52.0   IRanges_2.24.1         S4Vectors_0.28.1       Biobase_2.50.0         BiocGenerics_0.36.1   
[13] clusterProfiler_3.18.1 ReactomePA_1.34.0      influential_2.2.3      concaveman_1.1.0       ggforce_0.3.3          randomcoloR_1.1.0.1   
[19] ggnewscale_0.4.5       ggnetwork_0.5.10       igraph_1.2.6           STRINGdb_2.2.2         plyr_1.8.6             stringr_1.4.0         
[25] ggplot2_3.3.5          maftools_2.6.05       

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                    proto_1.0.0                   tidyselect_1.1.1              htmlwidgets_1.5.3             grid_4.0.3                   
  [6] BiocParallel_1.24.1           Rtsne_0.15                    scatterpie_0.1.6              munsell_0.5.0                 preprocessCore_1.52.1        
 [11] codetools_0.2-18              ragg_1.1.3                    chron_2.3-56                  withr_2.4.2                   colorspace_2.0-2             
 [16] GOSemSim_2.16.1               knitr_1.33                    rstudioapi_0.13               DOSE_3.16.0                   labeling_0.4.2               
 [21] polyclip_1.10-0               bit64_4.0.5                   farver_2.1.0                  downloader_0.4                vctrs_0.3.8                  
 [26] generics_0.1.0                xfun_0.24                     BiocFileCache_1.14.0          R6_2.5.0                      doParallel_1.0.16            
 [31] clue_0.3-59                   graphlayouts_0.7.1            bitops_1.0-7                  cachem_1.0.5                  fgsea_1.16.0                 
 [36] assertthat_0.2.1              promises_1.2.0.1              scales_1.1.1                  vroom_1.5.3                   nnet_7.3-16                  
 [41] ggraph_2.0.5                  enrichplot_1.10.2             gtable_0.3.0                  Cairo_1.5-12.2                tidygraph_1.2.0              
 [46] rlang_0.4.11                  systemfonts_1.0.2             GlobalOptions_0.1.2           splines_4.0.3                 lazyeval_0.2.2               
 [51] impute_1.64.0                 checkmate_2.0.0               BiocManager_1.30.16           yaml_2.2.1                    reshape2_1.4.4               
 [56] backports_1.2.1               httpuv_1.6.1                  Hmisc_4.5-0                   qvalue_2.22.0                 tools_4.0.3                  
 [61] tcltk_4.0.3                   ellipsis_0.3.2                gplots_3.1.1                  RColorBrewer_1.1-2            gsubfn_0.7                   
 [66] Rcpp_1.0.7                    hash_2.2.6.1                  base64enc_0.1-3               purrr_0.3.4                   RCurl_1.98-1.3               
 [71] rpart_4.1-15                  sqldf_0.4-11                  GetoptLong_1.0.5              viridis_0.6.1                 cowplot_1.1.1                
 [76] ggrepel_0.9.1                 cluster_2.1.2                 magrittr_2.0.1                data.table_1.14.0             DO.db_2.9                    
 [81] circlize_0.4.13               reactome.db_1.74.0            matrixStats_0.60.0            hms_1.1.0                     mime_0.11                    
 [86] xtable_1.8-4                  jpeg_0.1-9                    gridExtra_2.3                 shape_1.4.6                   compiler_4.0.3               
 [91] tibble_3.1.3                  KernSmooth_2.23-20            V8_3.4.2                      crayon_1.4.1                  shadowtext_0.0.8             
 [96] htmltools_0.5.1.1             later_1.2.0                   tzdb_0.1.2                    Formula_1.2-4                 tidyr_1.1.3                  
[101] DBI_1.1.1                     tweenr_1.0.2                  ExperimentHub_1.16.1          dbplyr_2.1.1                  ComplexHeatmap_2.6.2         
[106] MASS_7.3-54                   rappdirs_0.3.3                Matrix_1.3-4                  readr_2.0.0                   cli_3.0.1                    
[111] pkgconfig_2.0.3               rvcheck_0.1.8                 foreign_0.8-81                plotly_4.9.4.1                foreach_1.5.1                
[116] digest_0.6.27                 graph_1.68.0                  fastmatch_1.1-3               htmlTable_2.2.1               curl_4.3.2                   
[121] shiny_1.6.0                   gtools_3.9.2                  graphite_1.36.0               rjson_0.2.20                  lifecycle_1.0.0              
[126] jsonlite_1.7.2                viridisLite_0.4.0             fansi_0.5.0                   pillar_1.6.2                  lattice_0.20-44              
[131] fastmap_1.1.0                 httr_1.4.2                    plotrix_3.8-1                 survival_3.2-11               GO.db_3.12.1                 
[136] interactiveDisplayBase_1.28.0 glue_1.4.2                    zip_2.2.0                     png_0.1-7                     iterators_1.0.13             
[141] BiocVersion_3.12.0            bit_4.0.4                     stringi_1.7.3                 blob_1.2.2                    textshaping_0.3.5            
[146] AnnotationHub_2.22.1          latticeExtra_0.6-29           caTools_1.18.2                memoise_2.0.0                 dplyr_1.0.7
PPI STRINGdb • 73 views
Entering edit mode

Sorry for the late reply. The error should have been fixed by now.


Login before adding your answer.

Traffic: 358 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6